Peptides and combination of peptides for use in immunotherapy against ovarian cancer and other cancers

ABSTRACT

The present invention relates to peptides, proteins, nucleic acids and cells for use in immunotherapeutic methods. In particular, the present invention relates to the immunotherapy of cancer. The present invention furthermore relates to tumor-associated T-cell peptide epitopes, alone or in combination with other tumor-associated peptides that can for example serve as active pharmaceutical ingredients of vaccine compositions that stimulate anti-tumor immune responses, or to stimulate T cells ex vivo and transfer into patients. Peptides bound to molecules of the major histocompatibility complex (MHC), or peptides as such, can also be targets of antibodies, soluble T-cell receptors, and other binding molecules.

CROSS REFERENCE TO RELATED APPLICATIONS

This application is a continuation of U.S. patent application Ser. No.15/881,078, filed 26 Jan. 2018, which claims priority to U.S.Provisional Application No. 62/451,255, filed 27 Jan. 2017, and GermanPatent Application No. 10 2017 101671.6, filed 27 Jan. 2017, thecontents of which are incorporated herein by reference in theirentirety.

This application is also related to PCT/EP2018/051952 filed 26 Jan.2018, the content of which is incorporated herein by reference in itsentirety.

REFERENCE TO SEQUENCE LISTING SUBMITTED AS A COMPLIANT ASCII TEXT FILE(.txt)

Pursuant to the EFS-Web legal framework and 37 CFR §§ 1.821-825 (seeMPEP § 2442.03(a)), a Sequence Listing in the form of an ASCII-complianttext file (entitled “Sequence_Listing_2912919-083002_ST25.txt” createdon 5 Mar. 2020, and 132,646 bytes in size) is submitted concurrentlywith the instant application, and the entire contents of the SequenceListing are incorporated herein by reference.

FIELD

The present invention relates to peptides, proteins, nucleic acids andcells for use in immunotherapeutic methods. In particular, the presentinvention relates to the immunotherapy of cancer. The present inventionfurthermore relates to tumor-associated T-cell peptide epitopes, aloneor in combination with other tumor-associated peptides that can forexample serve as active pharmaceutical ingredients of vaccinecompositions that stimulate anti-tumor immune responses, or to stimulateT cells ex vivo and transfer into patients. Peptides bound to moleculesof the major histocompatibility complex (MHC), or peptides as such, canalso be targets of antibodies, soluble T-cell receptors, and otherbinding molecules.

The present invention relates to several novel peptide sequences andtheir variants derived from HLA class I and HLA class II molecules ofhuman tumor cells that can be used in vaccine compositions for elicitinganti-tumor immune responses, or as targets for the development ofpharmaceutically/immunologically active compounds and cells.

DESCRIPTION OF RELATED ART

Ovarian Cancer

With an estimated 239 000 new cases in 2012, ovarian cancer is theseventh most common cancer in women, representing 4% of all cancers inwomen. The fatality rate of ovarian cancer tends to be rather highrelative to other cancers of the female reproductive organs, and casefatality is higher in lower-resource settings. Therefore, ovarian canceris the eighth most frequent cause of cancer death among women, with 152000 deaths. In 2012, almost 55% of all new cases occurred in countrieswith high or very high levels of human development; 37% of the new casesand 39% of the deaths occurred in Europe and North America. Incidencerates are highest in northern and eastern Europe, North America, andOceania, and tend to be relatively low in Africa and much of Asia.Incidence rates have been declining in certain countries with very highlevels of human development, notably in Europe and North America.

The most common ovarian cancers are ovarian carcinomas, which are alsothe most lethal gynecological malignancies. Based on histopathology andmolecular genetics, ovarian carcinomas are divided into five main types:high-grade serous (70%), endometrioid (10%), clear cell (10%), mucinous(3%), and low-grade serous carcinomas (<5%), which together account formore than 95% of cases. Much less common are malignant germ cell tumors(dysgerminomas, yolk sac tumors, and immature teratomas) (3% of ovariancancers) and potentially malignant sex cord stromal tumors (1-2%), themost common of which are granulosa cell tumors.

Ovarian carcinomas most commonly affect nulliparous women and occurleast frequently in women with suppressed ovulation, typically bypregnancy or oral contraceptives. These tumors are generally consideredto originate from the cells covering the ovarian surface or the pelvicperitoneum. Malignant transformation of this mesothelium has beenexplained by the “incessant ovulation” theory (La, 2001).

Family history of ovarian cancer accounts for 10% of cases; the risk isincreased 3-fold when two or more first-degree relatives have beenaffected. Women with germline mutations in BRCA1 or BRCA2 have a 30-70%risk of developing ovarian cancer, mainly high-grade serous carcinomas,by age 70 (Risch et al., 2006).

Surgical resection is the primary therapy in early as well as advancedstage ovarian carcinoma. The ultimate goal is the complete removal ofthe tumor mass in healthy surrounding tissue. Surgical removal isfollowed by systemic chemotherapy with platinum analogs, except for verylow grade ovarian cancers (stage IA, grade 1), where post-operativechemotherapy is not indicated. In advanced stage, ovarian cancer, thefirst line chemotherapy comprises a combination of carboplatin withpaclitaxel, which can be supplemented with bevacizumab. The standardtreatment for platinum-resistant ovarian cancers consists of amonotherapy with one of the following chemotherapeutics: pegylatedliposomal doxorubicin, topotecane, gemcitabine or paclitaxel(S3-Leitlinie maligne Ovarialtumore, 2013).

Immunotherapy appears to be a promising strategy to ameliorate thetreatment of ovarian cancer patients, as the presence ofpro-inflammatory tumor infiltrating lymphocytes, especially CD8-positiveT cells, correlates with good prognosis and T cells specific fortumor-associated antigens can be isolated from cancer tissue.

Therefore, a lot of scientific effort is put into the investigation ofdifferent immunotherapies in ovarian cancer. A considerable number ofpre-clinical and clinical studies has already been performed and furtherstudies are currently ongoing. Clinical data are available for cytokinetherapy, vaccination, monoclonal antibody treatment, adoptive celltransfer and immunomodulation.

Cytokine therapy with interleukin-2, interferon-alpha, interferon-gammaor granulocyte-macrophage colony stimulating factor aims at boosting thepatient's own anti-tumor immune response and these treatments havealready shown promising results in small study cohorts.

Phase I and II vaccination studies, using single or multiple peptides,derived from several tumor-associated proteins (Her2/neu, NY-ESO-1, p53,Wilms tumor-1) or whole tumor antigens, derived from autologous tumorcells revealed good safety and tolerability profiles, but only low tomoderate clinical effects.

Monoclonal antibodies that specifically recognize tumor-associatedproteins are thought to enhance immune cell-mediated killing of tumorcells. The anti-CA-125 antibodies oregovomab and abagovomab as well asthe anti-EpCAM antibody catumaxomab achieved promising results in phaseII and III studies. In contrast, the anti-MUC1 antibody HMFG1 failed toclearly enhance survival in a phase III study.

An alternative approach uses monoclonal antibodies to target and blockgrowth factor and survival receptors on tumor cells. Whileadministration of trastuzumab (anti-HER2/neu antibody) and MOv18 andMORAb-003 (anti-folate receptor alpha antibodies) only conferred limitedclinical benefit to ovarian cancer patients, addition of bevacizumab(anti-VEGF antibody) to the standard chemotherapy in advanced ovariancancer appears to be advantageous.

Adoptive transfer of immune cells achieved heterogeneous results inclinical trials. Adoptive transfer of autologous, in vitro expandedtumor infiltrating T cells was shown to be a promising approach in apilot trial. In contrast, transfer of T cells harboring a chimericantigen receptor specific for folate receptor alpha did not induce asignificant clinical response in a phase I trial. Dendritic cells pulsedwith tumor cell lysate or tumor-associated proteins in vitro were shownto enhance the anti-tumor T cell response upon transfer, but the extentof T cell activation did not correlate with clinical effects. Transferof natural killer cells caused significant toxicities in a phase IIstudy.

Intrinsic anti-tumor immunity as well as immunotherapy are hampered byan immunosuppressive tumor microenvironment. To overcome this obstacleimmunomodulatory drugs, like cyclophosphamide, anti-CD25 antibodies andpegylated liposomal doxorubicin are tested in combination withimmunotherapy. Most reliable data are currently available foripilimumab, an anti-CTLA4 antibody, which enhances T cell activity.Ipilimumab was shown to exert significant anti-tumor effects in ovariancancer patients (Mantia-Smaldone et al., 2012).

Considering the severe side-effects and expense associated with treatingcancer, there is a need to identify factors that can be used in thetreatment of cancer in general and ovarian cancer in particular. Thereis also a need to identify factors representing biomarkers for cancer ingeneral and ovarian cancer in particular, leading to better diagnosis ofcancer, assessment of prognosis, and prediction of treatment success.

Immunotherapy of cancer represents an option of specific targeting ofcancer cells while minimizing side effects. Cancer immunotherapy makesuse of the existence of tumor associated antigens.

The current classification of tumor associated antigens (TAAs) comprisesthe following major groups:

a) Cancer-testis antigens: The first TAAs ever identified that can berecognized by T cells belong to this class, which was originally calledcancer-testis (CT) antigens because of the expression of its members inhistologically different human tumors and, among normal tissues, only inspermatocytes/spermatogonia of testis and, occasionally, in placenta.Since the cells of testis do not express class I and II HLA molecules,these antigens cannot be recognized by T cells in normal tissues and cantherefore be considered as immunologically tumor-specific. Well-knownexamples for CT antigens are the MAGE family members and NY-ESO-1.b) Differentiation antigens: These TAAs are shared between tumors andthe normal tissue from which the tumor arose. Most of the knowndifferentiation antigens are found in melanomas and normal melanocytes.Many of these melanocyte lineage-related proteins are involved inbiosynthesis of melanin and are therefore not tumor specific butnevertheless are widely used for cancer immunotherapy. Examples include,but are not limited to, tyrosinase and Melan-A/MART-1 for melanoma orPSA for prostate cancer.c) Over-expressed TAAs: Genes encoding widely expressed TAAs have beendetected in histologically different types of tumors as well as in manynormal tissues, generally with lower expression levels. It is possiblethat many of the epitopes processed and potentially presented by normaltissues are below the threshold level for T-cell recognition, whiletheir over-expression in tumor cells can trigger an anticancer responseby breaking previously established tolerance. Prominent examples forthis class of TAAs are Her-2/neu, survivin, telomerase, or WT1.d) Tumor-specific antigens: These unique TAAs arise from mutations ofnormal genes (such as β-catenin, CDK4, etc.). Some of these molecularchanges are associated with neoplastic transformation and/orprogression. Tumor-specific antigens are generally able to induce strongimmune responses without bearing the risk for autoimmune reactionsagainst normal tissues. On the other hand, these TAAs are in most casesonly relevant to the exact tumor on which they were identified and areusually not shared between many individual tumors. Tumor-specificity (or-association) of a peptide may also arise if the peptide originates froma tumor- (-associated) exon in case of proteins with tumor-specific(-associated) isoforms.e) TAAs arising from abnormal post-translational modifications: SuchTAAs may arise from proteins which are neither specific noroverexpressed in tumors but nevertheless become tumor associated byposttranslational processes primarily active in tumors. Examples forthis class arise from altered glycosylation patterns leading to novelepitopes in tumors as for MUC1 or events like protein splicing duringdegradation which may or may not be tumor specific.f) Oncoviral proteins: These TAAs are viral proteins that may play acritical role in the oncogenic process and, because they are foreign(not of human origin), they can evoke a T-cell response. Examples ofsuch proteins are the human papilloma type 16 virus proteins, E6 and E7,which are expressed in cervical carcinoma.

T-cell based immunotherapy targets peptide epitopes derived fromtumor-associated or tumor-specific proteins, which are presented bymolecules of the major histocompatibility complex (MHC). The antigensthat are recognized by the tumor specific T lymphocytes, that is, theepitopes thereof, can be molecules derived from all protein classes,such as enzymes, receptors, transcription factors, etc. which areexpressed and, as compared to unaltered cells of the same origin,usually up-regulated in cells of the respective tumor.

There are two classes of MHC-molecules, MHC class I and MHC class II.MHC class I molecules are composed of an alpha heavy chain andbeta-2-microglobulin, MHC class II molecules of an alpha and a betachain. Their three-dimensional conformation results in a binding groove,which is used for non-covalent interaction with peptides.

MHC class I molecules can be found on most nucleated cells. They presentpeptides that result from proteolytic cleavage of predominantlyendogenous proteins, defective ribosomal products (DRIPs) and largerpeptides. However, peptides derived from endosomal compartments orexogenous sources are also frequently found on MHC class I molecules.This non-classical way of class I presentation is referred to ascross-presentation in the literature (Brossart and Bevan, 1997; Rock etal., 1990). MHC class II molecules can be found predominantly onprofessional antigen presenting cells (APCs), and primarily presentpeptides of exogenous or transmembrane proteins that are taken up byAPCs e.g. during endocytosis, and are subsequently processed.

Complexes of peptide and MHC class I are recognized by CD8-positive Tcells bearing the appropriate T-cell receptor (TCR), whereas complexesof peptide and MHC class II molecules are recognized byCD4-positive-helper-T cells bearing the appropriate TCR. It is wellknown that the TCR, the peptide and the MHC are thereby present in astoichiometric amount of 1:1:1.

CD4-positive helper T cells play an important role in inducing andsustaining effective responses by CD8-positive cytotoxic T cells. Theidentification of CD4-positive T-cell epitopes derived from tumorassociated antigens (TAA) is of great importance for the development ofpharmaceutical products for triggering anti-tumor immune responses(Gnjatic et al., 2003). At the tumor site, T helper cells, support acytotoxic T cell- (CTL-) friendly cytokine milieu (Mortara et al., 2006)and attract effector cells, e.g. CTLs, natural killer (NK) cells,macrophages, and granulocytes (Hwang et al., 2007).

In the absence of inflammation, expression of MHC class II molecules ismainly restricted to cells of the immune system, especially professionalantigen-presenting cells (APC), e.g., monocytes, monocyte-derived cells,macrophages, dendritic cells. In cancer patients, cells of the tumorhave been found to express MHC class II molecules (Dengjel et al.,2006).

Elongated (longer) peptides of the invention can act as MHC class IIactive epitopes.

T-helper cells, activated by MHC class II epitopes, play an importantrole in orchestrating the effector function of CTLs in anti-tumorimmunity. T-helper cell epitopes that trigger a T-helper cell responseof the TH1 type support effector functions of CD8-positive killer Tcells, which include cytotoxic functions directed against tumor cellsdisplaying tumor-associated peptide/MHC complexes on their cellsurfaces. In this way tumor-associated T-helper cell peptide epitopes,alone or in combination with other tumor-associated peptides, can serveas active pharmaceutical ingredients of vaccine compositions thatstimulate anti-tumor immune responses.

It was shown in mammalian animal models, e.g., mice, that even in theabsence of CD8-positive T lymphocytes, CD4-positive T cells aresufficient for inhibiting manifestation of tumors via inhibition ofangiogenesis by secretion of interferon-gamma (IFNγ) (Beatty andPaterson, 2001; Mumberg et al., 1999). There is evidence for CD4 T cellsas direct anti-tumor effectors (Braumuller et al., 2013; Tran et al.,2014).

Since the constitutive expression of HLA class II molecules is usuallylimited to immune cells, the possibility of isolating class II peptidesdirectly from primary tumors was previously not considered possible.However, Dengjel et al. were successful in identifying a number of MHCClass II epitopes directly from tumors (WO 2007/028574, EP 1 760 088B1).

Since both types of response, CD8 and CD4 dependent, contribute jointlyand synergistically to the anti-tumor effect, the identification andcharacterization of tumor-associated antigens recognized by either CD8+T cells (ligand: MHC class I molecule+peptide epitope) or byCD4-positive T-helper cells (ligand: MHC class II molecule+peptideepitope) is important in the development of tumor vaccines.

For an MHC class I peptide to trigger (elicit) a cellular immuneresponse, it also must bind to an MHC-molecule. This process isdependent on the allele of the MHC-molecule and specific polymorphismsof the amino acid sequence of the peptide. MHC-class-I-binding peptidesare usually 8-12 amino acid residues in length and usually contain twoconserved residues (“anchors”) in their sequence that interact with thecorresponding binding groove of the MHC-molecule. In this way, each MHCallele has a “binding motif” determining which peptides can bindspecifically to the binding groove.

In the MHC class I dependent immune reaction, peptides not only have tobe able to bind to certain MHC class I molecules expressed by tumorcells, they subsequently also have to be recognized by T cells bearingspecific T cell receptors (TCR).

For proteins to be recognized by T-lymphocytes as tumor-specific or-associated antigens, and to be used in a therapy, particularprerequisites must be fulfilled. The antigen should be expressed mainlyby tumor cells and not, or in comparably small amounts, by normalhealthy tissues. In a preferred embodiment, the peptide should beover-presented by tumor cells as compared to normal healthy tissues. Itis furthermore desirable that the respective antigen is not only presentin a type of tumor, but also in high concentrations (i.e. copy numbersof the respective peptide per cell). Tumor-specific and tumor-associatedantigens are often derived from proteins directly involved intransformation of a normal cell to a tumor cell due to their function,e.g. in cell cycle control or suppression of apoptosis. Additionally,downstream targets of the proteins directly causative for atransformation may be up-regulated and thus may be indirectlytumor-associated. Such indirect tumor-associated antigens may also betargets of a vaccination approach (Singh-Jasuja et al., 2004). It isessential that epitopes are present in the amino acid sequence of theantigen, in order to ensure that such a peptide (“immunogenic peptide”),being derived from a tumor associated antigen, leads to an in vitro orin vivo T-cell-response.

Basically, any peptide able to bind an MHC molecule may function as aT-cell epitope. A prerequisite for the induction of an in vitro or invivo T-cell-response is the presence of a T cell having a correspondingTCR and the absence of immunological tolerance for this particularepitope.

Therefore, TAAs are a starting point for the development of a T cellbased therapy including but not limited to tumor vaccines. The methodsfor identifying and characterizing the TAAs are usually based on the useof T-cells that can be isolated from patients or healthy subjects, orthey are based on the generation of differential transcription profilesor differential peptide expression patterns between tumors and normaltissues. However, the identification of genes over-expressed in tumortissues or human tumor cell lines, or selectively expressed in suchtissues or cell lines, does not provide precise information as to theuse of the antigens being transcribed from these genes in an immunetherapy. This is because only an individual subpopulation of epitopes ofthese antigens are suitable for such an application since a T cell witha corresponding TCR has to be present and the immunological tolerancefor this particular epitope needs to be absent or minimal. In a verypreferred embodiment of the invention it is therefore important toselect only those over- or selectively presented peptides against whicha functional and/or a proliferating T cell can be found. Such afunctional T cell is defined as a T cell, which upon stimulation with aspecific antigen can be clonally expanded and is able to executeeffector functions (“effector T cell”).

In case of targeting peptide-MHC by specific TCRs (e.g. soluble TCRs)and antibodies or other binding molecules (scaffolds) according to theinvention, the immunogenicity of the underlying peptides is secondary.In these cases, the presentation is the determining factor.

SUMMARY OF THE INVENTION

In a first aspect of the present invention, the present inventionrelates to a peptide comprising an amino acid sequence selected from thegroup consisting of SEQ ID NO: 1 to SEQ ID NO: 772 or a variant sequencethereof which is at least 77%, preferably at least 88%, homologous(preferably at least 77% or at least 88% identical) to SEQ ID NO: 1 toSEQ ID NO: 772, wherein said variant binds to MHC and/or induces T cellscross-reacting with said peptide, or a pharmaceutical acceptable saltthereof, wherein said peptide is not the underlying full-lengthpolypeptide.

The present invention further relates to a peptide of the presentinvention comprising a sequence that is selected from the groupconsisting of SEQ ID NO: 1 to SEQ ID NO: 772 or a variant thereof, whichis at least 77%, preferably at least 88%, homologous (preferably atleast 77% or at least 88% identical) to SEQ ID NO: 1 to SEQ ID NO: 772,wherein said peptide or variant thereof has an overall length of between8 and 100, preferably between 8 and 30, and most preferred of between 8and 14 amino acids.

BRIEF DESCRIPTION OF THE DRAWINGS

The patent or application file contains at least one drawing executed incolor. Copies of this patent or patent application publication withcolor drawing(s) will be provided by the Office upon request and paymentof the necessary fee.

FIGS. 1A-9B depict embodiments as described herein.

DETAILED DESCRIPTION OF A PREFERRED EMBODIMENT

The following tables show the peptides according to the presentinvention, their respective SEQ ID NOs, and the prospective source(underlying) genes for these peptides. In Table 1, peptides with SEQ IDNO: 1 to SEQ ID NO: 9 bind to HLA-A*02, peptides with SEQ ID NO: 10 toSEQ ID NO: 19 bind to HLA-A*24, peptides with SEQ ID NO: 20 to SEQ IDNO: 30 bind to HLA-A*03, peptide with SEQ ID NO: 31 binds to HLA-A*01,peptides with SEQ ID NO: 32 to SEQ ID NO: 41 bind to HLA-B*07, peptideswith SEQ ID NO: 42 to SEQ ID NO: 51 bind to HLA-B*08, peptides with SEQID NO: 52 to SEQ ID NO: 59 bind to HLA-B*44. In Table 2, peptides withSEQ ID NO: 60 to SEQ ID NO: 75 bind to HLA-A*02, peptides with SEQ IDNO: 76 to SEQ ID NO: 82 bind to HLA-A*24, peptides with SEQ ID NO: 83 toSEQ ID NO: 111 bind to HLA-A*03, peptides with SEQ ID NO: 112 to SEQ IDNO: 116 bind to HLA-A*01, peptides with SEQ ID NO: 117 to SEQ ID NO: 149bind to HLA-B*07, peptides with SEQ ID NO: 150 to SEQ ID NO: 172 bind toHLA-B*08, peptides with SEQ ID NO: 173 to SEQ ID NO: 215 bind toHLA-B*44. In Table 3, peptides with SEQ ID NO: 216 to SEQ ID NO: 245bind to HLA-A*02, peptides with SEQ ID NO: 246 to SEQ ID NO: 255 bind toHLA-A*24, peptides with SEQ ID NO: 256 to SEQ ID NO: 287 bind toHLA-A*03, peptides with SEQ ID NO: 288 to SEQ ID NO: 292 bind toHLA-A*01, peptides with SEQ ID NO: 293 to SEQ ID NO: 392 bind toHLA-B*07, peptides with SEQ ID NO: 393 to SEQ ID NO: 395 bind toHLA-B*08, peptides with SEQ ID NO: 396 to SEQ ID NO: 438 bind toHLA-B*44. In Table 4, peptides with SEQ ID NO: 439 to SEQ ID NO: 551bind to several HLA class I alleles, peptide with SEQ ID NO: 773 bindsto HLA-A*02, peptide with SEQ ID NO: 774 binds to HLA-A*24. In Table 5,peptides with SEQ ID NO: 552 to SEQ ID NO: 772 bind to several HLA classII alleles.

TABLE 1  Peptides according to the present invention. Seq ID HLA NoSequence Gene Uniprot Accession allotype 1 MIPTFTALL LILRB4 Q8NHJ6 A*022 TLLKALLEI IDO1 P14902 A*02 3 ALIYNLVGI ATP7A, ATP7B, P35670 A*02CTAGE1 4 ALFKAWAL IRF4 Q15306 A*02 5 RLLDFINVL OVGP1 Q12889 A*02 6SLGKHTVAL OVGP1 Q12889 A*02 7 ALQAFEFRV PCDHB5, PCDHB15, Q9Y5E7 A*02PCDHB11, PCDHB10, PCDHB9, PCDHB8, PCDHB7, PCDHB4, PCDHB3, PCDHB2,PCDHB16 8 YLVTKVVAV PCDHGA12, PCDHB5, O60330, Q96TA0, A*02PCDHB1, PCDHB18, Q9NRJ7, Q9UN66, PCDHGB7, PCDHGB6, O9UN67, Q9UN71,PCDHGB5, PCDHGB3, Q9Y5E1, Q9Y5E2, PCDHGB2, PCDHGB1, Q9Y5E3, Q9Y5E4,PCDHGA11, Q9Y5E5, Q9Y5E6, PCDHGA10, PCDHGA9, Q9Y5E7, Q9Y5E8,PCDHGA7, PCDHGA6, Q9Y5E9, Q9Y5F0, PCDHGA5, PCDHGA4, Q9Y5F1, Q9Y5F2,PCDHGA3, PCDHGA2, Q9Y5F3, Q9Y5F8, PCDHGA1, PCDHGB8P, Q9Y5F9, Q9Y5G0,PCDHB15, PCDHB14, Q9Y5G1, Q9Y5G2, PCDHB13, PCDHB12, Q9Y5G3, Q9Y5G4,PCDHB11, PCDHB10, Q9Y5G5, Q9Y5G6, PCDHB9, PCDHB8, Q9Y5G7, Q9Y5G8,PCDHB7, PCDHB6, Q9Y5G9, Q9Y5H0, PCDHB4, PCDHB3, Q9Y5H1, Q9Y5H2,PCDHB2, PCDHB16, Q9Y5H3, Q9Y5H4 PCDHGB4, PCDHGA8 9 VLLAGFKPPL RNF17Q9BXT8 A*02 10 RYSDSVGRVSF CAPN13 Q6MZZ7 A*24 11 SYSDLHYGF CAPN13 Q6MZZ7A*24 12 KYEKIFEML CT45A3, CT45A4, Q5DJT8 A*24 CT45A5, CT45A6,CT45A1, CT45A2 13 VYTFLSSTL ESR1 P03372 A*24 14 FYFPTPTVL FOLR1 P15328A*24 15 VYHDDKQPTF GXYLT2 A0PJZ3 A*24 16 IYSPQFSRL MYO3B Q8WXR4 A*24 17RFTTMLSTF OVGP1 Q12889 A*24 18 KYPVHIYRL RAD54B Q9Y620 A*24 19 KYVKVFHQFZNF90, ZNF93, ZNF486 Q96H40 A*24 20 RMASPVNVK C2orf88 Q9BSF0 A*03 21AVRKPIVLK CDCA5 Q96FF9 A*03 22 SLKERNPLK CDH3 P22223 A*03 23 GMMKGGIRKESR1 P03372 A*03 24 SMYYPLQLK GXYLT2 A0PJZ3 A*03 25 GTSPPSVEK MUC16Q8WXI7 A*03 26 RISEYLLEK MY03B Q8WXR4 A*03 27 VLYGPAGLGK NLRP2 Q9NX02A*03 28 KTYETNLEIKK NLRP7 Q8WX94 A*03 29 QQFLTALFY NLRP7, NLRP2 Q8WX94A*03 30 ALEVAHRLK ZBTB12 Q9Y330 A*03 31 LLDEGAMLLY NLRP7 Q8WX94 A*O1 32SPNKGTLSV BCAM P50895 B*07 33 SPTFHLTL BCAM P50895 B*07 34 LPRGPLASLLCDH3 P22223 B*07 35 FPDNQRPAL ETV4 P43268 B*07 36 APAAWLRSA MMP11 P24347B*07/B*55 37 RPLFQKSSM MUC16 Q8WXI7 B*07 38 SPHPVTALLTL MUC16 Q8WXI7B*07 39 RPAPFEVVF NXNL2 Q5VZ03 B*07 40 KPGTSYRVTL SPON1 Q9HCB6 B*07 41RVRSRISNL TCEA1P2, TCEA1, Q15560 B*07 TCEA2, TCEA3 42 TLKVTSAL BCAMP50895 B*08 43 ALKARTVTF CCR2, CCR5 P51681 B*08 44 LNKQKVTFCTAGE4, CTAGE5 O15320 B*08 45 VGREKKLAL CTAGE4, CTAGE5 O15320 B*08 46DMKKAKEQL FUNDC2P2, Q9BWH2 B*08 FUNDC2P3, FUNDC2 47 MPNLRSVDL LRRTM1Q86UE6 B*08 48 DVKKKIKEV MFN1 Q8IWA4 B*08 49 LPRLKAFMI ST6GALNAC5 Q9BVH7B*08 50 DMKYKNRV TCEA1P2, TCEA1, Q15560 B*08 TCEA2 51 SLRLKNVQL VTCN1Q7Z7D3 B*08 52 AEFLLRIFL CAPN13 Q6MZZ7 B*44 53 MEHPGKLLF ESR1 P03372B*44 54 AEITITTQTGY MUC16 Q8WXI7 B*44 55 HETETRTTW MUC16 Q8WXI7 B*44 56SEPDTTASW MUC16 Q8WXI7 B*44 57 QESDLRLFL NLRP7, NLRP2 Q9NX02 B*44 58GEMEQKQL PNOC Q13519 B*44 59 SENVTMKVV VTCN1 Q7Z7D3 B*44

TABLE 2  Additional peptides according to the present invention. Seq IDHLA No Sequence Gene Uniprot Accession allotype 60 GLLSLTSTLYL BCAMP50895 A*02 61 YMVHIQVTL CD70 P32970 A*02 62 KVLGVNVML CRABP2 P29373A*02 63 MMEEMIFNL EYA2 O00167 A*02 64 FLDPDRHFL FAM83H Q6ZRV2 A*02 65TMFLRETSL GUCY1A2 P33402 A*02 66 GLLQELSSI HTR3A P46098 A*02 67SLLLPSIFL HTR3A P46098 A*02 68 KLFDTQQFL IRF4 O15306 A*02 69 TTYEGSITVMUC16 Q8WXI7 A*02 70 VLQGLLRSL MUC16 Q8WXI7 A*02 71 YLEDTDRNL NFE2L3Q9Y4A8 A*02 72 YLTDLQVSL NFE2L3 Q9Y4A8 A*02 73 FLIEELLFA OVGP1 Q12889A*02 74 SQSPSVSQL FRAME P78395 A*02 75 KVVSVLYNV VTCN1 Q7Z7D3 A*02 76KYVAELSLL CCNA1 P78396 A*24 77 RYGPVFTV CYP2W1 Q8TAV3 A*24 78 SFAPRSAVFHOXD9 P28356 A*24 79 SYNEHWNYL LTBR P36941 A*24 80 TAYMVSVAAF SDK2Q58EX2 A*24 81 VYNHTTRPL SPINT1 O43278 A*24 82 SYFRGFTLI SPON1 Q9HCB6A*24 83 GTYAHTVNR ALPI, ALPP, ALPPL2 P05187, P09923 A*03/A*31 84KLQPAQTAAK ALPP, ALPPL2 P05187 A*03 85 VLLGSLFSRK BCL2L1 O07817 A*03 86VVLLGSLFSRK BCL2L1 O07817 A*03/A*31/ A*66 87 AVAPPTPASK CBX2 Q14781A*03/A*11 88 VVHAVFALK CCR5 P51681 A*03 89 RVAELLLLH CDKN2A, CDKN2BP42771, P42772 A*03 90 KVAGERYVYK ETV1, ETV4, ETV5 P41161, P43268, A*03P50549 91 RSLRYYYEK ETV1, ETV4, ETV5 P43268 A*03 92 SVFPIENIY EYA2O00167 A*03 93 KILEEHTNK FSBP, RAD54B O95073 A*03 94 ATFERVLLR GUCY1A2P33402 A*03/A*11 95 QSMYYPLQLK GXYLT2 A0PJZ3 A*03 96 TAFGGFLKY LAMA1P25391 A*03 97 TMLDVEGLFY LAMA1 P25391 A*03 98 LLQPPPLLAR MMP11 P24347A*03 99 KVVDRWNEK MRPL51 Q4U2R6 A*03 100 RLFTSPIMTK MUC16 Q8WXI7 A*03101 RVFTSSIKTK MUC16 Q8WXI7 A*03 102 SVLTSSLVK MUC16 Q8WXI7 A*03 103TSRSVDEAY MUC16 Q8WXI7 A*03 104 VLADSVTTK MUC16 Q8WXI7 A*03 105RLFSWLVNR MYO1B Q8WXR4 A*03 106 AAFVPLLLK NCAPD2 Q15021 A*03/A*11 107RLQEWKALK PDCL2 Q8N4E4 A*03 108 VLYPVPLESY PRAME P78395 A*03 109KTFTIKRFLAK RPL39L Q96EH5 A*03 110 SAAPPSYFR SPON1 Q9HCB6 A*03/A*11/A*66 111 TLPQFRELGY WNT7A O00755 A*03 112 TVTGAEQIQY CAPN13 Q6MZZ7 A*O1113 QLDSNRLTY LRRTM1 Q86UE6 A*O1 114 VMEQSAGIMY LYPD1 Q8N2G4 A*O1 115FVDNQYWRY MMP12 P39900 A*O1 116 VLLDEGAMLLY NLRP7 Q8WX94 A*O1 117APRLLLLAVL BCAM P50895 B*07 118 SPASRSISL CD70 P32970 B*07 119APLPRPGAVL CTAG2 O75638 B*07 120 RPAMNYDKL ETV1, ETV4, ETV5, P43268 B*07SPDEF 121 VPNQSSESL EYA2 O00167 B*07/B*35 122 YPGFPQSQY EYA2 O00167B*07/B*35 123 KPSESIYSAL FAM111B Q6SJ93 B*07 124 LPSDSHFKITF FAM111BQ6SJ93 B*07 125 VPVYILLDEM FAM83H Q6ZRV2 B*07/B*35 126 KPGPEDKLFOLR1, FOLR2 P15328 B*07 127 APRAGSQVV FUNDC2 Q9BWH2 B*07 128 YPRTITPGMKLK14 Q9P0G3 B*07 129 APRPASSL MMP11 P24347 B*07 130 FPRLVGPDF MMP11P24347 B*07 131 APTEDLKAL MSLN Q13421 B*07 132 IPGPAQSTI MUC16 Q8WXI7B*07 133 MPNLPSTTSL MUC16 Q8WXI7 B*07 134 RPIVPGPLL MUC16 Q8WXI7 B*07135 RVRSTISSL MUC16 Q8WXI7 B*07 136 SPFSAEEANSL MUC16 Q8WXI7 B*07 137SPGATSRGTL MUC16 Q8WXI7 B*07 138 SPMATTSTL MUC16 Q8WXI7 B*07 139SPQSMSNTL MUC16 Q8WXI7 B*07 140 SPRTEASSAVL MUC16 Q8WXI7 B*07 141SPMTSLLTSGL MUC16 Q8WXI7 B*07 142 TPGLRETSI MUC16 Q8WXI7 B*07 143SPAMTSTSF MUC16 Q8WXI7 B*07/B*35 144 SPSPVSSTL MUC16 Q8WXI7 B*07/B*35145 SPSSPMSTF MUC16 Q8WXI7 B*07/B*35 146 IPRPEVQAL PLEKHG4 O58EX7 B*07147 APRWFPQPTVV VTCN1 O7Z7D3 B*07 148 KPYGGSGPL ZNF217 O75362 B*07 149GPREALSRL ZSCAN30, ZNF263, O14978, O43309, B*07 ZNF500, ZKSCAN4,O60304, P17029, ZNF323, ZKSCAN1, P49910, Q16670, ZNF165, ZNF187,Q86W11, Q8NF99, ZKSCAN3, ZNF397, Q969J2, Q96LW9, ZSCAN12 Q9BRRO 150MAAVKQAL BCL2L1 Q07817 B*08 151 HLLLKVLAF CCNA1 P78396 B*08 152MGSARVAEL CDKN2A, CDKN2B P42771 B*08 153 NAMLRKVAV CRABP1 P29762 B*08154 MLRKIAVAA CRABP2 P29373 B*08 155 NKKMMKRLM DPPA2 Q7Z7J5 B*08 156HVKEKFLL FAM83H Q6ZRV2 B*08 157 EAMKRLSYI LAMC2 Q13753 B*08 158 LPKLAGLLLINC0O176 Q6ZNR8 B*08/B*07 159 VLKHKLDEL MSLN Q13421 B*08 160 YPKARLAFMSLN Q13421 B*08 161 ALKTTTTAL DNAJC22, MUC16 Q8WXI7 B*08 162 QAKTHSTLMUC16 Q8WXI7 B*08 163 QGLLRPVF MUC16 Q8WXI7 B*08 164 SIKTKSAEM MUC16Q8WXI7 B*08 165 SPRFKTGL MUC16 Q8WXI7 B*08 166 TPKLRETSI MUC16 Q8WXI7B*08 167 TSHERLTTL MUC16 Q8WXI7 B*08 168 TSHERLTTY MUC16 Q8WXI7 B*08 169TSMPRSSAM MUC16 Q8WXI7 B*08 170 YLLEKSRVI MYO3B, MYH15, MYH6, A7E2Y1, B0I1T2, B*08 MYH7, MYO1D, MY03A,  O94832, P12883, MYH7BP13533, Q8NEV4, Q8WXR4, Q9Y2K3 171 FAFRKEAL OVGP1 Q12889 B*08 172KLKERNREL OVGP1 Q12889 B*08 173 AEAQVGDERDY BCAM P50895 B*44 174AEATARLNVF BCAM P50895 B*44 175 AEIEPKADG BCAM P50895 B*44 176AEIEPKADGSW BCAM P50895 B*44 177 TEVGTMNLF BCAT1 P54687 B*44 178NELFRDGVNW BCL2L1 Q07817 B*44 179 REAGDEFEL BCL2L1 Q07817 B*44 180REAGDEFELRY BCL2L1 Q07817 B*44 181 GEGPKTSW CRABP2 P29373 B*44 182KEATEAQSL CTAGE4, CTAGE10P, Q96RT6 B*44/B*40 CTAGE16P, CTAGE5, CTAGE1183 YEKGIMQKV ETV1, ETV4, ETV5 P43268 B*44/B*49 184 AELEALTDLW EYA2O00167 B*44 185 AERQPGAASL FAM83H Q6ZRV2 B*44 186 REGPEEPGL FAM83HQ6ZRV2 B*44 187 GEAQTRIAW FOLR1 P15328 B*44 188 AEFAKKQPWW FUNDC2 Q9BWH2B*44 189 KEFLFNMY HOXA9, HOXA10, P28356 B*44 HOXB9, HOXC9,HOXC10, HOXD9, HOXD10 190 YEVARILNL HOXD9 P28356 B*44 191 EEDAALFKAWIRF4 Q15306 B*44 192 YEFKFPNRL LGALS1 P09382 B*44/B*18/ B*40 193LEAQQEAL MAGEA1, MRPL40 P43355 B*44 194 KEVDPTSHSY MAGEA11 P43364 B*44195 AEDKRHYSV MFN1 Q8IWA4 B*44 196 REMPGGPVW MMP12 P39900 B*44 197AEVLLPRLV MSLN O13421 B*44 198 QEAARAAL MSLN O13421 B*44 199 REIDESLIFYMSLN O13421 B*44 200 AESIPTVSF MUC16 Q8WXI7 B*44 201 AETILTFHAF MUC16Q8WXI7 B*44 202 HESEATASW MUC16 Q8WXI7 B*44 203 IEHSTQAQDTL MUC16 Q8WXI7B*44 204 RETSTSEETSL MUC16 Q8WXI7 B*44 205 SEITRIEM MUC16 Q8WXI7 B*44206 SESVTSRTSY MUC16 Q8WXI7 B*44 207 TEARATSDSW MUC16 Q8WXI7 B*44 208TEVSRTEAI MUC16 Q8WXI7 B*44 209 TEVSRTEL MUC16 Q8WXI7 B*44 210VEAADIFQNF NXNL2 Q5VZ03 B*44 211 EEKVFPSPLW PNOC Q13519 B*44 212MEQKQLQKRF PNOC Q13519 B*44 213 KESIPRWYY SPINT1 O43278 B*44 214VEQTRAGSLL TDRD5 Q8NAT2 B*44 215 SEDGLPEGIHL ZNF217 O75362 B*44

TABLE 3  Additional peptides according to the present invention. Seq IDHLA No Sequence Gene Uniprot Accession allotype 216 IMFDDAIERAALPP, ALPPL2 P05187 A*02 217 VSSSLTLKV BCAM P50895 A*02 218 TIASQRLTPLCD70 P32970 A*02 219 PLPRPGAVL CTAG2 O75638 A*02 220 RMTTQLLLL FOLR1P15328 A*02/B*13 221 SLLDLYQL FTHL17 Q9BXU8 A*02/B*35 222 ALMRLIGCPLGPC2 Q8N158 A*02 223 FAHHGRSL IRF4 Q15306 A*02 224 SLPRFQVTL IRF4 Q15306A*02 225 SVFAHPRKL MAGEA2B, MAGEA2, P43365 A*02 MAGEA6, MAGEA12 226QVDPKKRISM MELK Q14680 A*02 227 YTFRYPLSL MMP11 P24347 A*02 228RLWDWVPLA MRPL51 Q4U2R6 A*02 229 ISVPAKTSL MUC16 Q8WXI7 A*02 230SAFREGTSL MUC16 Q8WXI7 A*02 231 SVTESTHHL MUC16 Q8WXI7 A*02 232TISSLTHEL MUC16 Q8WXI7 A*02 233 GSDTSSKSL MUC16 Q8WXI7 A*02/B*14 234GVATRVDAI MUC16 Q8WXI7 A*02/B*14 235 SAIETSAVL MUC16 Q8WXI7 A*02/B*35236 SAIPFSMTL MUC16 Q8WXI7 A*02/B*35 237 SAMGTISIM MUC16 Q8WXI7A*02/B*35 238 PLLVLFTI MUC16 Q8WXI7 A*02/B*51 239 FAVPTGISM MUC16 Q8WXI7A*02/C*03 240 FSTDTSIVL MUC16 Q8WXI7 A*02/C*03 241 RQPNILVHL MUC16Q8WXI7 A*02:05 242 STIPALHEI MUC16 Q8WXI7 A*02:05 243 YASEGVKQV SPON1Q9HCB6 A*02/B*51 244 DTDSSVHVQV TENM4 Q6N022 A*02 245 LAVEGGQSL UBXN8O00124 A*02 246 RYLAVVHAVF CCR5 P51681 A*24/A*23 247 ARPPWMWVL KLK5Q9Y337 A*24/B*27 248 SVIQHLGY MSLN Q13421 A*24 249 VYTPTLGTLDNAJC22, MUC16 Q8WXI7 A*24 250 HFPEKTTHSF MUC16 Q8WXI7 A*24/C*14 251KQRQVLIFF PCDHB2 Q9Y5E7 A*24/B*15 252 LYQPRASEM PNOC Q13519 A*24/A*25253 AYPEIEKF PTTG2, PTTG1 O95997 A*24/C*04 254 IIQHLTEQF STAG3 Q9UJ98A*24/C*03 255 VFVSFSSLF ZNF560 Q96MR9 A*24/B*27 256 RTEEVLLTFK GPR64Q8IZP9 A*03 257 VTADHSHVF ALPI, ALPL, ALPP, P05187 A*03 258 GAYAHTVNRALPPL2 P10696 A*03 259 KTLELRVAY BCAM P50895 A*03/A*32 260 GTNTVILEYC2orf88 Q9BSF0 A*03 261 HTFGLFYQR FAM111B Q6SJ93 A*03 262 RSRLNPLVQRFAM83H Q6ZRV2 A*03 263 SSSSATISK HOXD3 P31249 A*03/A*11 264 AIKVIPTVFKIDO1 P14902 A*03 265 QIHDHVNPK IDO1 P14902 A*03/A*11 266 ISYSGQFLVKIGF2BP1 Q9NZI8 A*03 267 VTDLISPRK LAMA1 P25391 A*03 268 GLLGLSLRY LRRTM1Q86UE6 A*03/A*11/ A*29 269 RLKGDAWVYK MELK Q14680 A*03 270 AVFNPRFYRTYMMP12 P39900 A*03/A*11 271 RMFADDLHNLNK MRPL51 Q4U2R6 A*03 272RQPERTILRPR MSLN Q13421 A*03 273 RVNAIPFTY MSLN Q13421 A*03/A*26 274KTFPASTVF MUC16 Q8WXI7 A*03 275 STTFPTLTK MUC16 Q8WXI7 A*03 276VSKTTGMEF MUC16 Q8WXI7 A*03 277 TTALKTTSR DNAJC22, MUC16 Q8WXI7A*03/A*66 278 NLSSITHER MUC16 Q8WXI7 A*03/A*68 279 SVSSETTKIKR MUC16Q8WXI7 A*03/A*68 280 SVSGVKTTF MUC16 Q8WXI7 A*03/B*15 281 RAKELEATFNLRP7, NLRP2 09NX02 A*03 282 CLTRTGLFLRF NLRP7, NLRP2 Q9NX02 A*03 283IVQEPTEEK PAGE2, PAGE2B Q7Z2X7 A*03/A*11 284 KSLIKSWKK TCEA1P2, TCEA1, P23193, Q15560 A*03/A*11 TCEA2 285 GTVNPTVGK TENM4 Q6N022 A*03/A*11 286TVAPPQGVVK ZBTB12 Q9Y330 A*03/A*68 287 RRIHTGEKPYK ZNF271, KLF8, ZNF816,Q8IW36 A*03/A*11 ZFP28, ZSCAN29, ZNF597, ZNF480, ZNF714, ZNF836,ZNF600, ZNF320, ZNF100, ZNF721, ZNF841, ZNF678, ZNF860, ZNF429,ZNF888, ZNF761, ZNF701, ZNF83, ZNF695, ZNF471, ZNF22, ZNF28,ZNF137P, ZNF665, ZNF606, ZNF430, ZNF34, ZNF616, ZNF468, ZNF160,ZNF765, ZNF845 288 SPVTSVHGGTY LILRB4 Q8NHJ6 A*01/B*35 289 RWEKTDLTYMMP11 P24347 A*01 290 DMDEEIEAEY MY03B Q8WXR4 A*01/A*25 291 ETIRSVGYYTENM4 Q6N022 A*01/A*25 292 NVTMKVVSVLY VTCN1 Q7Z7D3 A*01 293 VPDSGATATAYALPP, ALPPL2 P05187 B*07/B*35 294 YPLRGSSIF ALPP, ALPPL2 P05187B*07/B*35 295 YPLRGSSIFGL ALPP, ALPPL2 P05187 B*07/B*35 296 YPLRGSSIALPP, ALPPL2 P05187 B*51/B*07 297 TVREASGLL BCAM P50895 B*07 298YPTEHVQF BCAM P50895 B*07/B*35 299 HPGSSALHY BCAT1 P54687 B*07/B*35 300IPMAAVKQAL BCL2L1 Q07817 B*07 301 SPRRSPRISF CDCA5 Q96FF9 B*07 302RVEEVRALL CDKN2A P42771 B*07 303 LPMWKVTAF CLDN6 P56747 B*07 304LPRPGAVL CTAG2 O75638 B*07 305 TPWAESSTKF DPEP3 Q9H4B8 B*07/B*35 306APVIFSHSA DPEP2, DPEP3 Q9H4B8 B*55/B*56/ B*07 307 LPYGPGSEAAAF ESR1P03372 B*07/B*35 308 YPEGAAYEF ESR1 P03372 B*07/B*35 309 FPQSQYPQY EYA2O00167 B*07/B*35 310 RPNPITIIL FBN2 P35556 B*07 311 RPLFYVVSL HTR3AP46098 B*07 312 LPYFREFSM HTR3A P46098 B*07/B*35 313 KVKSDRSVF HTR3AP46098 B*15/B*07 314 VPDQPHPEI IRF4 Q15306 B*07/B*35 315 SPRENFPDTL KLK8O60259 B*07 316 EPKTATVL LAMA1 P25391 B*42/B*07 317 FPFQPGSV LGALS1P09382 B*51/B*07 318 FPNRLNLEA LGALS1 P09382 B*54/B*55/ B*07 319SPAEPSVYATL LILRB4 Q8NHJ6 B*07 320 FPMSPVTSV LILRB4 Q8NHJ6 B*07/B*51 321SPMDTFLLI LILRB4 Q8NHJ6 B*51/B*07 322 SPDPSKHLL LRRK1 Q385D2 B*07/B*35323 RPMPNLRSV LRRTM1 Q86UE6 B*55/B*07 324 VPYRVVGL MEX3D, MEX3C, A1L020B*51/B*07 MEX3B, MEX3A 325 GPRNAQRVL MFN1 Q8IWA4 B*07 326 VPSEIDAAFMMP11 P24347 B*07/B*35 327 SPLPVTSLI MUC16 Q8WXI7 B*07 328 EPVTSSLPNFMUC16 Q8WXI7 B*07/B*35 329 FPAMTESGGMIL MUC16 Q8WXI7 B*07/B*35 330FPFVTGSTEM MUC16 Q8WXI7 B*07/B*35 331 FPHPEMTTSM MUC16 Q8WXI7 B*07/B*35332 FPHSEMTTL MUC16 Q8WXI7 B*07/B*35 333 FPHSEMTTVM MUC16 Q8WXI7B*07/B*35 334 FPYSEVTTL MUC16 Q8WXI7 B*07/B*35 335 HPDPVGPGL MUC16Q8WXI7 B*07/B*35 336 HPKTESATPAAY MUC16 Q8WXI7 B*07/B*35 337 HPVETSSALMUC16 Q8WXI7 B*07/B*35 338 HVTKTQATF MUC16 Q8WXI7 B*07/B*35 339LPAGTTGSLVF MUC16 Q8WXI7 B*07/B*35 340 LPEISTRTM MUC16 Q8WXI7 B*07/B*35341 LPLDTSTTL MUC16 Q8WXI7 B*07/B*35 342 LPLGTSMTF MUC16 Q8WXI7B*07/B*35 343 LPSVSGVKTTF MUC16 Q8WXI7 B*07/B*35 344 LPTQTTSSL MUC16Q8WXI7 B*07/B*35 345 LPTSESLVSF MUC16 Q8WXI7 B*07/B*35 346 LPWDTSTTLFMUC16 Q8WXI7 B*07/B*35 347 MPLTTGSQGM MUC16 Q8WXI7 B*07/B*35 348MPNSAIPFSM MUC16 Q8WXI7 B*07/B*35 349 MPSLSEAMTSF MUC16 Q8WXI7 B*07/B*35350 NPSSTTTEF MUC16 Q8WXI7 B*07/B*35 351 NVLTSTPAF MUC16 Q8WXI7B*07/B*35 352 SPAETSTNM MUC16 Q8WXI7 B*07/B*35 353 SPAMTTPSL MUC16Q8WXI7 B*07/B*35 354 SPLPVTSLL MUC16 Q8WXI7 B*07/B*35 355 SPLVTSHIMMUC16 Q8WXI7 B*07/B*35 356 SPNEFYFTV MUC16 Q8WXI7 B*07/B*35 357SPSPVPTTL MUC16 Q8WXI7 B*07/B*35 358 SPSPVTSTL MUC16 Q8WXI7 B*07/B*35359 SPSTIKLTM MUC16 Q8WXI7 B*07/B*35 360 SPSVSSNTY MUC16 Q8WXI7B*07/B*35 361 SPTHVTQSL MUC16 Q8WXI7 B*07/B*35 362 SPVPVTSLF MUC16Q8WXI7 B*07/B*35 363 TAKTPDATF MUC16 Q8WXI7 B*07/B*35 364 TPLATTQRFMUC16 Q8WXI7 B*07/B*35 365 TPLATTQRFTY MUC16 Q8WXI7 B*07/B*35 366TPLTTTGSAEM MUC16 Q8WXI7 B*07/B*35 367 TPSVVTEGF MUC16 Q8WXI7 B*07/B*35368 VPTPVFPTM MUC16 Q8WXI7 B*07/B*35 369 FPHSEMTTV MUC16 Q8WXI7B*07/B*35/ B*51 370 PGGTRQSL MUC16 Q8WXI7 B*14:02/ B*07 371 LYVDGFTHWMUC16 Q8WXI7 B*35/B*55/ B*07 372 IPRNPPPTLL MYO3B Q8WXR4 B*07 373RPRALRDLRIL NLRP7, NLRP2 Q9NX02 B*07 374 NPIGDTGVKF NLRP7 Q8WX94B*07/B*35 375 AAASPLLLL NMU P48645 B*07 376 RPRSPAGQVA NMU P48645B*07/B*55 377 RPRSPAGQVAAA NMU P48645 B*07/B*55 378 RPRSPAGQVAA NMUP48645 B*07/B*56 379 GPFPLVYVL OVGP1 Q12889 B*07/B*35 380 IPTYGRTF OVGP1Q12889 B*07/B*35 381 LPEQTPLAF OVGP1 Q12889 B*07/B*35 382 SPMHDRWTFOVGP1 Q12889 B*07/B*35 383 TPTKETVSL OVGP1 Q12889 B*07/B*35 384YPGLRGSPM OVGP1 Q12889 B*07/B*35 385 SPALHIGSV PCDHB5, PCDHB18,Q96TA0, Q9NRJ7, B*07 PCDHB17, PCDHB15, Q9UN66, Q9UN67, PCDHB14, PCDHB11,Q9Y5E1, Q9Y5E3, PCDHB10, PCDHB9, Q9Y5E4, Q9Y5E5, PCDHB8, PCDHB6,Q9Y5E6, Q9Y5E7, PCDHB4, PCDHB3, Q9Y5E8, Q9Y5E9, PCDHB2, PCDHB16 Q9Y5F2386 FPFNPLDF PTTG1 O95997 B*07/B*35 387 APLKLSRTPA SPON1 Q9HCB6B*07/B*55 388 SPAPLKLSRTPA SPON1 Q9HCB6 B*07/B*55/ B*56 389 SPGAQRTFFQLSTAG3, STAG3L3, P0CL83, Q9UJ98 B*07 STAG3L2, STAG3L1 390 NPDLRRNVL TCEA2Q15560 B*07 391 APSTPRITTF TCEA2 Q15560 B*07 392 KPIESTLVA TMEM158Q8WZ71 B*07/B*55 393 ASKPHVEI CRABP1 P29762 B*08 394 MYKMKKPI MAGEB3O15480 B*08 395 VLLPRLVSC MSLN Q13421 B*08/A*02 396 REASGLLSL BCAMP50895 B*44 397 REGDTVQLL BCAM P50895 B*44 398 SFEQVVNELF BCL2L1 Q07817B*44 399 RELLHLVTL CAPN13 Q6MZZ7 B*44/B*37 400 GEIEIHLL CCDC146 Q81YE0B*44/B*40 401 EDLKEELLL CPXCR1 08N123 B*44/B*18 402 RELANDELIL CRABP1P29762 B*44 403 EEAQWVRKY FAM111B Q6SJ93 B*44 404 NEAIMHQY FAM111BQ6SJ93 B*44/B*18 405 NEIWTHSY F0LR1 P15328 B*44/B*18 406 EDGRLVIEF FRAS1Q86XX4 B*44/B*18 407 AEHEGVSVL GXYLT2 A0PJZ3 B*44 408 LEKALQVF ID01P14902 B*44 409 REFVLSKGDAGL ID01 P14902 B*44 410 SEDPSKLEA ID01 P14902B*44 411 LELPPILVY ID01 P14902 B*44/B*18 412 QEILTQVKQ IGF2BP3 O00425B*44/B*40 413 IEALSGKIEL IGF2BP3 O00425 B*44/B*45 414 EDAALFKAW IRF4Q15306 B*44 415 REEDAALFKAW IRF4 Q15306 B*44 416 SEEETRVVF MELK Q14680B*44 417 AEHFSMIRA MEX3C, MEX3B, A1L020, Q5U5Q3, B*44/B*50 MEX3A Q6ZN04418 FEDAQGHIW MMP11 P24347 B*44 419 HEFGHVLGL MMP11 P24347 B*44/B*40 420FESHSTVSA MUC16 Q8WXI7 B*44 421 GEPATTVSL MUC16 Q8WXI7 B*44 422SETTFSLIF MUC16 Q8WXI7 B*44 423 SEVPTGTTA MUC16 Q8WXI7 B*44 424TEFPLFSAA MUC16 Q8WXI7 B*44 425 SEVPLPMAI MUC16 Q8WXI7 B*44/B*18 426PEKTTHSF MUC16 Q8WXI7 B*44/ C*04:01 427 HESSSHHDL NFE2L3 Q9Y4A8 B*44 428LDLGLNHI NLRP2 Q9NX02 B*44/B*47 429 REKFIASVI OVG P1 Q12889 B*44 430DEKILYPEF OVGP1 Q12889 B*44/B*18 431 AEQDPDELNKA POMZP3, ZP3P21754, Q6PJE2 B*44/B*41 432 EEQYIAQF PRAME P78395 B*44/B*18 433SDSQVRAF STAG1, STAG3, STAG2 Q8N3U4, Q8WVM7, B*44/B*37 Q9UJ98 434KEAIREHQM TCEA1P2, TCEA1, P23193, Q15560 B*44/B*41 TCEA2 435 REEFVSIDHLTMPRSS3 P57727 B*44 436 REPGDIFSEL WISP3 O95389 B*44 437 TEAVVTNEL XPR1Q9UBH6 B*44 438 SEVDSPNVL ZNF217 O75362 B*44

TABLE 4  HLA Class I peptides according to the present invention. Seq IDHLA No Sequence Gene Uniprot Accession allotype 439 EALAKLMSL ATP7BP35670 B*51 440 ELFEGLKAF BCAT1 P54687 A*25 441 HQITEVGTM BCAT1 P54687B*15 442 ILSKLTDIQY BCAT1 P54687 B*15 443 GTFNPVSLW BCAT1 P54687 B*58444 KLSQKGYSW BCL2L1 Q07817 A*32 445 LHITPGTAY BCL2L1 Q07817 B*13 446GRIVAFFSF BCL2L1 Q07817 B*27 447 MQVLVSRI BCL2L1 Q07817 B*52/B*13 448LSQKGYSW BCL2L1 Q07817 B*57 449 RAFSDLTSQL BCL2L1 Q07817 C*15 450KQTFPFPTI C2orf88 Q9BSF0 B*13 451 DYLNEWGSRF CDH3 P22223 A*23 452LKVLGVNVM CRABP2 P29373 C*07 453 DVKLEKPK DPPA2 Q7Z7J5 A*68 454AQTDPTTGY LOXL2, ENTPD4 Q9Y4K0 B*15 455 AAAANAQVY ESR1 P03372 B*35 456IPLERPLGEVY ESR1 P03372 B*35 457 NAAAAANAQVY ESR1 P03372 B*35 458TDTLIHLM ESR1 P03372 B*37 459 KVAGERYVY ETV1, ETV4, ETV5 P41161, P43268,A*32/A*31 P50549 460 RLSSATANALY FAM83H Q6ZRV2 A*26 461 AQRMTTQLL FOLR1P15328 B*15 462 QRMTTQLLL FOLR1 P15328 B*27/C*07 463 VNQSLLDLY FTHL17Q9BXU8 A*26 464 MSALRPLL GPC2 Q8N158 C*15 465 DLIESGQLR ID01 P14902 A*66466 DLIESGQLRER ID01 P14902 A*66 467 MQMQERDTL ID01 P14902 B*15 468ALAKLLPL KLK10 O43240 B*35 469 QEQSSVVRA KLK6 Q92876 B*45 470 QGERLLGAAVLAG3 P18627 C*03 471 AQRLDPVYF LAMC2 Q13753 B*15 472 MRLLVAPL LRRN2O75325 B*14 473 MLNNNALSAL LRRN2 O75325 B*35 474 AADGGLRASVTL LY6EQ16553 C*05 475 GRDPTSYPSL MAGEA11 P43364 B*39 476 ISYPPLHEWMAGEA3, MAGEA12 P43357 B*57 477 RIQQQTNTY MEX3A A1L020 B*15 478VVGPKGATI MEX3D, MEX3C, A1L020, Q5U503, C*14 MEX3B, MEX3A Q6ZN04, Q86XN8479 TEGSHFVEA MFN1 Q8IWA4 B*45 480 GRADIMIDF MMP11 P24347 B*27 481GRWEKTDLTY MMP11 P24347 B*27 482 GRWEKTDLTYR MMP11 P24347 B*27 483VRFPVHAALVW MMP11 P24347 B*27 484 AWLRSAAA MMP11 P24347 B*56 485VRFPVHAAL MMP11 P24347 C*07 486 DRFFWLKV MMP12 P39900 B*14 487 GMADILVVFMMP12 P39900 B*15 488 RSFSLGVPR MRPL51 Q4U2R6 A*31 489 EVSGLSTER MSLNQ13421 A*68 490 AEVQKLLGP MSLN Q13421 B*50 491 EAYSSTSSW MUC16 Q8WXI7A*25 492 EVTPWISLTL MUC16 Q8WXI7 A*25 493 DTNLEPVTR MUC16 Q8WXI7 A*68494 ETTASLVSR MUC16 Q8WXI7 A*68 495 EVPSGATTEVSR MUC16 Q8WXI7 A*68 496EVPTGTTAEVSR MUC16 Q8WXI7 A*68 497 EVSRTEVISSR MUC16 Q8WXI7 A*68 498EVYPELGTQGR MUC16 Q8WXI7 A*68 499 SSETTKIKR MUC16 Q8WXI7 A*68 500AHVLHSTL MUC16 Q8WXI7 B*14 501 IQIEPTSSL MUC16 Q8WXI7 B*14 502 SGDQGITSLMUC16 Q8WXI7 B*14 503 TVFDKAFTAA MUC16 Q8WXI7 B*14 504 TVSSVNQGL MUC16Q8WXI7 B*14 505 YVPTGAITQA MUC16 Q8WXI7 B*14 506 HQFITSTNTF MUC16 Q8WXI7B*15 507 TSIFSGQSL MUC16 Q8WXI7 B*15 508 TVAKTTTTF MUC16 Q8WXI7 B*15 509GRGPGGVSW MUC16 Q8WXI7 B*27 510 RRIPTEPTF MUC16 Q8WXI7 B*27 511SRIPQDVSW MUC16 Q8WXI7 B*27 512 SRSPENPSW MUC16 Q8WXI7 B*27 513SRTEISSSR MUC16 Q8WXI7 B*27 514 SRTEVASSR MUC16 Q8WXI7 B*27 515TRIEMESTF MUC16 Q8WXI7 B*27 516 TASTPISTF MUC16 Q8WXI7 B*35 517TAETILTFHAF MUC16 Q8WXI7 B*35 518 TSDFPTITV MUC16 Q8WXI7 B*35 519VTSLLTPGMV MUC16 Q8WXI7 B*35 520 THSAMTHGF MUC16 Q8WXI7 B*38 521THSTASQGF MUC16 Q8WXI7 B*38 522 THSTISQGF MUC16 Q8WXI7 B*38 523APKGIPVKPTSA MUC16 Q8WXI7 B*55 524 AVSPTVQGL MUC16 Q8WXI7 C*07 525QRFPHSEM MUC16 Q8WXI7 C*07 526 SVPDILST MUC16 Q8WXI7 C*07 527 QSTPYVNSVMUC16 Q8WXI7 C*16 528 TRTGLFLRF NLRP7, NLRP2 Q9NX02 B*27 529 PFSNPRVLNLRP2 Q9NX02 C*04 530 MLPRAALL NLRP7 Q8WX94 B*51 531 QGAQLRGALNLRP7, NLRP2 Q8WX94 B*52 532 AISFSYKAW OVGP1 Q12889 A*25 533 GQHLHLETFFRAME P78395 B*15 534 CRPGALQIEL RAD54B Q9Y620 C*02 535 IKDVRKIK RNF17Q9BXT8 B*13 536 VQDQACVAKF RNF17 Q9BXT8 B*15 537 IRRLKELKDQRPL37A, RPL37AP8 A6NKH3, P61513 n/a 538 QLEKALKEI SAGE1 Q9NXZ1 C*05 539IPIPSTGSVEM SPINT1 O43278 B*35/B*42 540 AGIPAVALW SPINT1 O43278 B*58 541RLSPAPLKL SPON1 Q9HCB6 B*13 542 QIIDEEETQF SPON1 Q9HCB6 B*15 543MRLSPAPLK SPON1 Q9HCB6 B*27 544 LRNPSIQKL SPON1 Q9HCB6 C*07 545 RVGPPLLITMEM158 Q8WZ71 B*15 546 GRAFFAAAF TMEM158 Q8WZ71 B*27 547 EVNKPGVYTRTMPRSS3 P57727 A*68 548 VSEASLVSSI ZBTB12 Q9Y330 C*05 549 ARSKLQQGLZNF217 O75362 B*27 550 RRFKEPWFL ZNF217, ZNF516, O15090, O75362, ZNF536Q92618 B*27 551 RLHTGEKPYK ZNF816, ZNF813, A2RRD8, A6NHJ4, A*30ZNF578, ZNF599, A6NK21, A6NK53, ZNF600, ZNF320, A6NK75, A6NN14,ZNF525, ZNF485, A6NNF4, A6NP11, ZNF860, ZNF429, A8MTY0, A8MUV8,ZNF808, ZNF888, B4DU55, B4DX44, ZNF761, ZNF701, B4DXR9, O14628,ZNF83, ZNF167, ZFP62, O14709, O15090, ZNF28, ZSCAN21, O43309, O43345,ZNF91, ZNF229, O43361, O75346, ZNF702P, ZNF528, O75373, O75437,ZNF468, ZNF765, O75820, O95600, ZNF845 O95780, P0CB33, P0CJ79, P0DKX0,P10073, P17019, P17026, P17035, P17038, P17040, P17097, P35789,P51522, P51815, P52742, Q02386, Q03923, Q03924, Q03936, Q03938,Q05481, Q08AN1, Q09FC8, Q0VGE8, Q14584, Q14586, Q14590, Q14591,Q14593, Q15928, Q15929, Q15937, Q16587, Q2M3W8, Q2M3X9, Q2VY69,Q3KP31, Q3MI56, Q3SXZ3, Q4V348, Q53GI3, Q5HY98, Q5JNZ3, Q5SXM1,Q5VIY5, Q5VV52, Q68DY1, Q6AZW8, Q6P280, Q6P9G9, Q6PDB4, Q6ZMV8,Q6ZMW2, Q6ZN06, Q6ZN08, Q6ZN19, Q6ZN57, Q6ZNA1, Q6ZNG1, Q6ZR52,Q76KX8, Q7L2R6, Q7L945, Q7Z3V5, Q7Z7L9, Q86TJ5, Q86UE3, Q86V71,Q86XN6, Q86XU0 Q86Y25, Q81W36, Q8IWY8, Q8IYN0, Q8IZ26, Q8N4W9,Q8N782, Q8N703, Q8N823, Q8N859, Q8N8C0, Q8N8J6, Q8N972, Q8N988,Q8N9F8, Q8NB50, Q8NCK3, Q8NDQ6, Q8NEM1, Q8NF99, Q8NHY6, Q8TAQ5,Q8TBZ5, Q8TD23, Q8TF20, Q8TF32, Q8TF39, Q8WV37, Q8WX64, Q96CX3,Q96IR2, Q96JC4, Q96LX8, Q96MR9, Q96N22, Q96N38, Q96N58, Q96NI8,Q96NL3, Q96PE6, Q96RE9, Q965E7, Q99676, Q9BX82, Q9H5H4, Q9H7R5,Q9H8G1, Q9H963, Q9HBT7, Q9HCG1, Q9HCL3, Q9NQX6, Q9NV72, Q9POL1,Q9P255, Q9P2F9, Q9P2J8, Q9UEG4, Q9U1I5, Q9UJW7, Q9UL36, Q9Y201,Q9Y473, Q9Y5A6 773 ALYGKLLKL VPS13B A*02 774 VYVDDIYVI CASC5 A*24

TABLE 5  HLA Class II peptides according to the present invention.Seq ID No Sequence Additional Sequence variants Gene 552GVNAMLRKVAVAAASKPHVE CRABP1 553 VNAMLRKVAVAAASKPHVE CRABP1 554GVNAMLRKVAVAAASKPH CRABP1 555 VNAMLRKVAVAAASKPH CRABP1 556NAMLRKVAVAAASKPH CRABP1 557 AMLRKVAVAAASKPH CRABP1 558 LRKVAVAAASKPHCRABP1 559 RKVAVAAASKPH CRABP1 560 PNFSGNWKIIRSENFEELLK CRABP1 561PNFSGNWKIIRSENFEELL CRABP2 562 GNWKIIRSENFEELLKVL CRABP2 563PNFSGNWKIIRSENFEEL CRABP2 564 GNWKIIRSENFEELLKV CRABP2 565NWKIIRSENFEELLKV CRABP2 566 NWKIIRSENFEELLK CRABP2 567 NWKIIRSENFEELLCRABP2 568 WKIIRSENFEELLK CRABP2 569 WKIIRSENFEELL CRABP2 570GNWKIIRSENF CRABP2 571 PNFSGNWKIIR CRABP2 572 INFKVGEEFEEQTV CRABP2 573RLLSADTKGWVRLQ DPPA2 574 LPDFYNDWMFIAKHLPDL IDO1 575 VGDDHLLLLQGEQLRRTKLK10 576 VGDDHLLLLQGEQLRR KLK10 577 GDDHLLLLQGEQLRR KLK10 578DDHLLLLQGEQLRR KLK10 579 SGGPLVCDETLQGILS KLK10 580 GGPLVCDETLQGILSKLK10 581 GGPLVCDETLQGIL KLK10 582 GSQPWQVSLFNGLSFH KLK10 583LTVKLPDGYEFKFPNRLNLEAIN LGALS1 584 TVKLPDGYEFKFPNRLNLEAINY LGALS1 585LTVKLPDGYEFKFPNRLNL LGALS1 586 TVKLPDGYEFKFPNRLNL LGALS1 587DQANLTVKLPDGYEFKFPNRLNL LGALS1 588 VAPDAKSFVLNLGKDSNNL LGALS1 589APDAKSFVLNLGKDSNNL LGALS1 590 RVRGEVAPDAKSFVLNLG LGALS1 591VRGEVAPDAKSFVLNL LGALS1 592 VRGEVAPDAKSFVLNLG LGALS1 593 GEVAPDAKSFVLNLGLGALS1 594 VRGEVAPDAKSFVLN LGALS1 595 VRGEVAPDAKSFVL LGALS1 596MAADGDFKIKCVAFD LGALS1 597 SPDAESLFREALSNKVDEL MAGEA4 598AESLFREALSNKVDEL MAGEA4 599 AESLFREALSNKVDE MAGEA4 600 FREALSNKVDEMAGEA4 601 LSNKVDELAHFLLRK MAGEA4 602 KDPVAWEAGMLMH MAGEB1 603KARDETRGLNVPQ MAGEB2 604 KLITQDLVKLKYLEYRQ MAGEB3 605LTVAEVQKLLGPHVEGLKAEERHRP MSLN 606 LTVAEVQKLLGPHVEGLKAEER MSLN 607LTVAEVQKLLGPHVEGLKAEE MSLN 608 LTVAEVQKLLGPHVEGLKAE MSLN 609LTVAEVQKLLGPHVEGLKA MSLN 610 LTVAEVQKLLGPHVEGLK MSLN 611LTVAEVQKLLGPHVEGL MSLN 612 TVAEVQKLLGPHVEGLK MSLN 613 LTVAEVQKLLGPHVEGMSLN 614 TVAEVQKLLGPHVEGL MSLN 615 VAEVQKLLGPHVEGLK MSLN 616TVAEVQKLLGPHVEG MSLN 617 VAEVQKLLGPHVEGL MSLN 618 VAEVQKLLGPHVEG MSLN619 VAEVQKLLGPHVE MSLN 620 EVQKLLGPHVEG MSLN 621 LTVAEVQKLLG MSLN 622MDALRGLLPVLGQPIIRSIPQGIVA MSLN 623 ALRGLLPVLGQPIIRSIPQGIVA MSLN 624LRGLLPVLGQPIIRSIPQGIVA MSLN 625 DALRGLLPVLGQPIIRSIPQG MSLN 626RGLLPVLGQPIIRSIPQGIVA MSLN 627 ALRGLLPVLGQPIIRSIPQG MSLN 628DALRGLLPVLGQPIIRSIPQ MSLN 629 GLLPVLGQPIIRSIPQGIVA MSLN 630ALRGLLPVLGQPIIRSIPQ MSLN 631 DALRGLLPVLGQPIIRSIP MSLN 632LLPVLGQPIIRSIPQGIVA MSLN 633 LRGLLPVLGQPIIRSIPQ MSLN 634DALRGLLPVLGQPIIRS MSLN 635 ALRGLLPVLGQPIIRS MSLN 636 DALRGLLPVLGQPIIRMSLN 637 ALRGLLPVLGQPIIR MSLN 638 LRGLLPVLGQPIIRS MSLN 639ALRGLLPVLGQPII MSLN 640 ALRGLLPVLGQPI MSLN 641 RGLLPVLGQPIIR MSLN 642GLLPVLGQPIIR MSLN 643 LRGLLPVLGQPI MSLN 644 RGLLPVLGQPI MSLN 645RGLLPVLGQPIIRSIPQGIVAAWRQ MSLN 646 GLLPVLGQPIIRSIPQGIVAAWRQ MSLN 647LPVLGQPIIRSIPQGIVAAWRQ MSLN 648 GLLPVLGQPIIRSIPQGIVAA MSLN 649LLPVLGQPIIRSIPQGIVAA MSLN 650 LPVLGQPIIRSIPQGIVAAW MSLN 651LPVLGQPIIRSIPQGIVAA MSLN 652 PVLGQPIIRSIPQGIVAAW MSLN 653LPVLGQPIIRSIPQGIVA MSLN 654 PVLGQPIIRSIPQGIVA MSLN 655 LGQPIIRSIPQGIVAAMSLN 656 VLGQPIIRSIPQGIVA MSLN 657 QPIIRSIPQGIVA MSLN 658VSTMDALRGLLPVLGQPIIRSIPQG MSLN 659 VSTMDALRGLLPVLGQPIIRSIPQ MSLN 660VSTMDALRGLLPVLGQPIIR MSLN 661 LRGLLPVLGQPIIRSIPQG MSLN 662LRTDAVLPLTVAEVQKLLGPHVEG MSLN 663 ERTDAVLPLTVAEVQKLLGPHVG MSLN 664AVLPLTVAEVQKLLGPHVEG MSLN 665 VLPLTVAEVQKLLGPHVEG MSLN 666LPLTVAEVQKLLGPHVEG MSLN 667 TDAVLPLTVAEVQ MSLN 668 AVLPLTVAEVQK MSLN 669VLPLTVAEVQKLLGPHVEGLKAEE MSLN 670 VLPLTVAEVQKLLGPHVEGLK MSLN 671LPLTVAEVQKLLGPHVEGLK MSLN 672 LRGLLPVLGQPIIRSIPQGIVAA MSLN 673IPFTYEQLDVLKHKLDELYPQ MSLN 674 IPFTYEQLDVLKHKLDE MSLN 675IPFTYEQLDVLKHKLD MSLN 676 VPPSSIWAVRPQDLDTCDPR MSLN 677 IWAVRPQDLDTCDPRMSLN 678 AVRPQDLDTCDPR MSLN 679 WGVRGSLLSEADVRALGGLA MSLN 680GVRGSLLSEADVRALGGLA MSLN 681 WGVRGSLLSEADVRALGGL MSLN 682GVRGSLLSEADVRALGGL MSLN 683 VRGSLLSEADVRALGGLA MSLN 684WGVRGSLLSEADVRALGG MSLN 685 GVRGSLLSEADVRALGG MSLN 686 VRGSLLSEADVRALGGLMSLN 687 WGVRGSLLSEADVRALG MSLN 688 GVRGSLLSEADVRALG MSLN 689WGVRGSLLSEADVRAL MSLN 690 GSLLSEADVRALGGL MSLN 691 GVRGSLLSEADVRAL MSLN692 RGSLLSEADVRALGG MSLN 693 WGVRGSLLSEADVRA MSLN 694 GSLLSEADVRALGGMSLN 695 RGSLLSEADVRALG MSLN 696 WGVRGSLLSEADVR MSLN 697 GSLLSEADVRALGMSLN 698 VRGSLLSEADVRA MSLN 699 LLSEADVRALGG MSLN 700 SLLSEADVRALG MSLN701 GSLLSEADVRA MSLN 702 LLSEADVRALG MSLN 703 LSEADVRALGG MSLN 704SEADVRALGG MSLN 705 EADVRALGG MSLN 706 LSTERVRELAVALAQKNVK MSLN 707LSTERVRELAVALAQKN MSLN 708 ERVRELAVALAQKNVK MSLN 709 LSTERVRELAVALAQKMSLN 710 LSTERVRELAVALAQ MSLN 711 STERVRELAVALAQK MSLN 712TERVRELAVALAQKN MSLN 713 VRELAVALAQKNVK MSLN 714 AIPFTYEQLDVLKHKLDE MSLN715 GLSTERVRELAVALAQKN MSLN 716 GLSTERVRELAVALAQ MSLN 717IPQGIVAAWRQRSSRDPS MSLN 718 GIVAAWRQRSSRDPS MSLN 719 IPQGIVAAWRQRSSRMSLN 720 ALGGLACDLPGRFVAES MSLN 721 RELAVALAQKNVKLSTE MSLN 722LKALLEVNKGHEMSPQ MSLN 723 TFMKLRTDAVLPLTVA MSLN 724 FMKLRTDAVLPLTVA MSLN725 FMKLRTDAVLPLT MSLN 726 FMKLRTDAVLPL MSLN 727 TLGLGLQGGIPNGYLV MSLN728 DLPGRFVAESAEVLL MSLN 729 DLPGRFVAESAEVL MSLN 730 LPGRFVAESAEVL MSLN731 DLPGRFVAESA MSLN 732 ERHRPVRDWILRQRQ MSLN 733 SPRQLLGFPCAEVSG MSLN734 SRTLAGETGQEAAPL MSLN 735 VTSLETLKALLEVNK MSLN 736 LGLQGGIPNGYLVLMSLN 737 LQGGIPNGYLVL MSLN 738 GGIPNGYLVL MSLN 739 LQGGIPNGYLVLDL MSLN740 APERQRLLPAALA MSLN 741 FVKIQSFLGGAPT MSLN 742 FVKIQSFLGG MSLN 743FVKIQSFLG MSLN 744 FLKMSPEDIRK MSLN 745 WELSQLTNSVTELGPYTLDRD MUC16 746EITITTQTGYSLATSQVTLP MUC16 747 ATTPSWVETHSIVIQGFPH MUC16 748GIKELGPYTLDRNSLYVNG MUC16 749 GIKELGPYTLDRNSL MUC16 750 GPYTLDRNSLYVNGMUC16 751 GIKELGPYTLDRN MUC16 752 LGPYTLDRNSLYV MUC16 753 LGPYTLDRNSLYMUC16 754 LGPYTLDRNSL MUC16 755 IELGPYLLDRGSLYVNG MUC16 756LGPYLLDRGSLYVNG MUC16 757 LGPYLLDRGSLYVN MUC16 758 LGPYLLDRGSLYV MUC16759 EELGPYTLDRNSLYVNG MUC16 760 LKPLFKSTSVGPLYSG MUC16 761LKPLFKSTSVGPLYS MUC16 762 LKPLFKSTSVGPLY MUC16 763 LKPLFKSTSVGPL MUC16764 FDKAFTAATTEVSRTE MUC16 765 ELGPYTLDRDSLYVN MUC16 766 GLLKPLFKSTSVGPLMUC16 767 LLKPLFKSTSVGPL MUC16 768 SDPYKATSAVVITST MUC16 769SDPYKATSAVVITS MUC16 770 SRKFNTMESVLQGLL MUC16 771 SRKFNTMESVLQG MUC16772 LGFYVLDRDSLFIN MUC16

The present invention furthermore generally relates to the peptidesaccording to the present invention for use in the treatment ofproliferative diseases, such as, for example, hepatocellular carcinoma,colorectal carcinoma, glioblastoma, gastric cancer, esophageal cancer,non-small cell lung cancer, small cell lung cancer, pancreatic cancer,renal cell carcinoma, prostate cancer, melanoma, breast cancer, chroniclymphocytic leukemia, Non-Hodgkin lymphoma, acute myeloid leukemia,gallbladder cancer and cholangiocarcinoma, urinary bladder cancer,uterine cancer, head and neck squamous cell carcinoma, mesothelioma.

Particularly preferred are the peptides—alone or incombination—according to the present invention selected from the groupconsisting of SEQ ID NO: 1 to SEQ ID NO: 772. More preferred are thepeptides—alone or in combination—selected from the group consisting ofSEQ ID NO: 1 to SEQ ID NO: 215 (see Tables 1 and 2), and their uses inthe immunotherapy of ovarian cancer, hepatocellular carcinoma,colorectal carcinoma, glioblastoma, gastric cancer, esophageal cancer,non-small cell lung cancer, small cell lung cancer, pancreatic cancer,renal cell carcinoma, prostate cancer, melanoma, breast cancer, chroniclymphocytic leukemia, Non-Hodgkin lymphoma, acute myeloid leukemia,gallbladder cancer and cholangiocarcinoma, urinary bladder cancer,uterine cancer, head and neck squamous cell carcinoma, mesothelioma, andpreferably ovarian cancer.

Thus, another aspect of the present invention relates to the use of thepeptides according to the present invention for the—preferablycombined—treatment of a proliferative disease selected from the group ofovarian cancer, hepatocellular carcinoma, colorectal carcinoma,glioblastoma, gastric cancer, esophageal cancer, non-small cell lungcancer, small cell lung cancer, pancreatic cancer, renal cell carcinoma,prostate cancer, melanoma, breast cancer, chronic lymphocytic leukemia,Non-Hodgkin lymphoma, acute myeloid leukemia, gallbladder cancer andcholangiocarcinoma, urinary bladder cancer, uterine cancer, head andneck squamous cell carcinoma, mesothelioma.

The present invention furthermore relates to peptides according to thepresent invention that have the ability to bind to a molecule of thehuman major histocompatibility complex (MHC) class-I or—in an elongatedform, such as a length-variant—MHC class-II.

The present invention further relates to the peptides according to thepresent invention wherein said peptides (each) consist or consistessentially of an amino acid sequence according to SEQ ID NO: 1 to SEQID NO: 772.

The present invention further relates to the peptides according to thepresent invention, wherein said peptide is modified and/or includesnon-peptide bonds.

The present invention further relates to the peptides according to thepresent invention, wherein said peptide is part of a fusion protein, inparticular fused to the N-terminal amino acids of the HLA-DRantigen-associated invariant chain (Ii), or fused to (or into thesequence of) an antibody, such as, for example, an antibody that isspecific for dendritic cells.

The present invention further relates to a nucleic acid, encoding thepeptides according to the present invention. The present inventionfurther relates to the nucleic acid according to the present inventionthat is DNA, cDNA, PNA, RNA or combinations thereof.

The present invention further relates to an expression vector capable ofexpressing and/or expressing a nucleic acid according to the presentinvention.

The present invention further relates to a peptide according to thepresent invention, a nucleic acid according to the present invention oran expression vector according to the present invention for use in thetreatment of diseases and in medicine, in particular in the treatment ofcancer.

The present invention further relates to antibodies that are specificagainst the peptides according to the present invention or complexes ofsaid peptides according to the present invention with MHC, and methodsof making these.

The present invention further relates to T-cell receptors (TCRs), inparticular soluble TCR (sTCRs) and cloned TCRs engineered intoautologous or allogeneic T cells, and functional fragments thereof, andmethods of making these, as well as NK cells or other cells bearing saidTCR or cross-reacting with said TCRs.

The antibodies and TCRs are additional embodiments of theimmunotherapeutic use of the peptides according to the presentinvention.

The present invention further relates to a host cell comprising anucleic acid according to the present invention or an expression vectoras described before. The present invention further relates to the hostcell according to the present invention that is an antigen presentingcell, and preferably is a dendritic cell.

The present invention further relates to a method for producing apeptide according to the present invention, said method comprisingculturing the host cell according to the present invention, andisolating the peptide from said host cell or its culture medium.

The present invention further relates to said method according to thepresent invention, wherein the antigen is loaded onto class I or II MHCmolecules expressed on the surface of a suitable antigen-presenting cellor artificial antigen-presenting cell by contacting a sufficient amountof the antigen with an antigen-presenting cell.

The present invention further relates to the method according to thepresent invention, wherein the antigen-presenting cell comprises anexpression vector capable of expressing or expressing said peptidecontaining SEQ ID No. 1 to SEQ ID No.: 772, preferably containing SEQ IDNo. 1 to SEQ ID No. 215, or a variant amino acid sequence.

The present invention further relates to activated T cells, produced bythe method according to the present invention, wherein said T cellselectively recognizes a cell which expresses a polypeptide comprisingan amino acid sequence according to the present invention.

The present invention further relates to a method of killing targetcells in a patient which target cells aberrantly express a polypeptidecomprising any amino acid sequence according to the present invention,the method comprising administering to the patient an effective numberof T cells as produced according to the present invention.

The present invention further relates to the use of any peptide asdescribed, the nucleic acid according to the present invention, theexpression vector according to the present invention, the cell accordingto the present invention, the activated T lymphocyte, the T cellreceptor or the antibody or other peptide- and/or peptide-MHC-bindingmolecules according to the present invention as a medicament or in themanufacture of a medicament. Preferably, said medicament is activeagainst cancer.

Preferably, said medicament is a cellular therapy, a vaccine or aprotein based on a soluble TCR or antibody.

The present invention further relates to a use according to the presentinvention, wherein said cancer cells are ovarian cancer, hepatocellularcarcinoma, colorectal carcinoma, glioblastoma, gastric cancer,esophageal cancer, non-small cell lung cancer, small cell lung cancer,pancreatic cancer, renal cell carcinoma, prostate cancer, melanoma,breast cancer, chronic lymphocytic leukemia, Non-Hodgkin lymphoma, acutemyeloid leukemia, gallbladder cancer and cholangiocarcinoma, urinarybladder cancer, uterine cancer, head and neck squamous cell carcinoma,mesothelioma, and preferably ovarian cancer cells.

The present invention further relates to biomarkers based on thepeptides according to the present invention, herein called “targets”that can be used in the diagnosis of cancer, preferably ovarian cancer.The marker can be over-presentation of the peptide(s) themselves, orover-expression of the corresponding gene(s). The markers may also beused to predict the probability of success of a treatment, preferably animmunotherapy, and most preferred an immunotherapy targeting the sametarget that is identified by the biomarker. For example, an antibody orsoluble TCR can be used to stain sections of the tumor to detect thepresence of a peptide of interest in complex with MHC.

Optionally the antibody carries a further effector function such as animmune stimulating domain or toxin.

The present invention also relates to the use of these novel targets inthe context of cancer treatment.

Both therapeutic and diagnostic uses against additional cancerousdiseases are disclosed in the following more detailed description of theunderlying expression products (polypeptides) of the peptides accordingto the invention.

ALPP, also known as ALP, PLAP or PALP, encodes an alkaline phosphatase,a metallo-enzyme that catalyzes the hydrolysis of phosphoric acidmonoesters (RefSeq, 2002). ALPP was described to be hyper-expressed invarious human tumors and their cell lines, particularly in cancers ofthe testis and ovary (Millan and Fishman, 1995). ALPP was identified asan independent prognostic factor for the survival of osteosarcomapatients which also correlates with lung metastasis. Furthermore, ALPPwas described as an immunohistochemical marker of gastrointestinalsmooth muscle neoplasms, germ cell tumor precursors, such as carcinomain situ and gonadoblastoma, and as a promising ovarian cancer biomarker(Ravenni et al., 2014; Wong et al., 2014b; Faure et al., 2016; Han etal., 2012).

ALPPL2, also known as GCAP, encodes a membrane bound glycosylatedenzyme, localized to testis, thymus and certain germ cell tumors, whichis closely related to both the placental and intestinal forms ofalkaline phosphatase (RefSeq, 2002). ALPPL2 was shown to be ectopicallyexpressed in seminoma as well as in many pancreatic cancer cell lines atboth mRNA and protein levels and to be involved in cancer cell growthand invasion. Additionally, ALPPL2 was described as a potentialdiagnostic marker of pancreatic ductal adenocarcinoma (Hofmann andMillan, 1993; Dua et al., 2013; Fishman, 1995). RT-PCR for ALPPL2 wasdescribed to be suitable for the sensitive detection of residual germcell tumor cells in peripheral blood and progenitor cell harvests(Hildebrandt et al., 1998).

BCAM encodes the basal cell adhesion molecule (Lutheran blood group), amember of the immunoglobulin superfamily and a receptor for theextracellular matrix protein, laminin (RefSeq, 2002). BCAM is a specificreceptor for laminin alpha5 (LAMAS), a subunit of laminin-511 (LM-511)that is a major component of basement membranes in various tissues; theBCAM/LAMAS system plays a functional role in the metastatic spreading ofKRAS-mutant colorectal cancer as well as in the migration ofhepatocellular carcinoma (Kikkawa et al., 2013; Kikkawa et al., 2014;Bartolini et al., 2016). Serum levels of BCAM were found to besignificantly increased in breast cancer patients and itsover-expression was found to be associated with skin, ovarian andpancreatic cancers as well as with endometrioid endometrial carcinoma,ovarian endometrioid carcinoma and cutaneous squamous cell carcinoma(Kikkawa et al., 2008; Planaguma et al., 2011; Latini et al., 2013; Kimet al., 2015a; Li et al., 2017). Being able to form a fusion proteinwith AKT2, BCAM was identified as AKT2 kinase activator in high-gradeserous ovarian cancer (Kannan et al., 2015).

CBX2 encodes chromobox 2 which is a component of the polycombmultiprotein complex, which is required to maintain thetranscriptionally repressive state of many genes throughout developmentvia chromatin remodeling and modification of histones (RefSeq, 2002).CBX2 is involved in cell proliferation and metastasis (Clermont et al.,2016). CBX2 is regulated by SMARCE1 leading to suppressed EGFRtranscription. CBX2 is involved in the regulation of three tumorsuppressor genes encoded in the INK4A/ARF locus (Papadakis et al., 2015;Agherbi et al., 2009; Miyazaki et al., 2008). CBX2 is over-expressed incancer including breast cancer, ovarian cancer, lung cancer, metastaticcastration-resistant and neuroendocrine prostate cancer and basal-likeendometrioid endometrial carcinoma (Parris et al., 2010; Clermont etal., 2016; Clermont et al., 2014; Clermont et al., 2015; Jiang et al.,2015; Xu et al., 2016). CBX2 is associated with lower patient survivaland metastatic progression. CBX2 is linked to peritumoral inflammatoryinfiltration, metastatic spread to the cervical lymph nodes, and tumorsize (Parris et al., 2014; Clermont et al., 2014; Xu et al., 2016). CBX2over-expression results in hematopoietic stem cell differentiation andexhaustion (Klauke et al., 2013).

CCNA1 encodes cyclin A1, which belongs to the highly conserved cyclinfamily involved in the regulation of CDK kinases (RefSeq, 2002).Elevated levels of CCNA1 were detected in epithelial ovarian cancer,lymphoblastic leukemic cell lines as well as in childhood acutelymphoblastic leukemia patients. Others have observed over-expression ofCCNA1 protein and mRNA in prostate cancer and in tumor tissues ofanaplastic thyroid carcinoma patients (Holm et al., 2006; Wegiel et al.,2008; Marlow et al., 2012; Arsenic et al., 2015). Recent studies haveshown that silencing of CCNA1 in highly cyclin A1 expressing ML1leukemic cells slowed S phase entry, decreased proliferation andinhibited colony formation (Ji et al., 2005).

CD70 encodes CD70 molecule which is a cytokine that belongs to the tumornecrosis factor (TNF) ligand family. It induces proliferation ofco-stimulated T cells, enhances the generation of cytolytic T cells, andcontributes to T cell activation. This cytokine is also reported to playa role in regulating B-cell activation, cytotoxic function of naturalkiller cells, and immunoglobulin synthesis (RefSeq, 2002). Targeting ofCD70 may be used to specifically target and kill cancer cells. It may bea potential target in oral cancer (Bundela et al., 2014; Jacobs et al.,2015b; Wang et al., 2016a). CD70 is expressed in head-and-neck squamouscell carcinoma. It is ectopically expressed in lymphomas, renal cellcarcinomas, and glioblastomas. CD70 expression levels decrease duringmelanoma progression. CD70 is highly expressed on CD4+CD25+ T-cells frompatients with acute-type adult T-cell leukemia/lymphoma (Jacobs et al.,2015b; Curran et al., 2015; De et al., 2016; Jacobs et al., 2015a;Masamoto et al., 2016; Pich et al., 2016b; Ruf et al., 2015a). CD70 isinvolved in immune response, cancer development, and cancer progression(Petrau et al., 2014; Pich et al., 2016a). CD70 up-regulation in clearcell renal cell carcinoma is associated with worse survival (Ruf et al.,2015b). Cisplatin mediates cytotoxicity through APCs expressingrelatively higher levels of CD70 (Beyranvand et al., 2016). CD70expression is almost not affected by ionizing radiation. It isassociated with radio sensitivity in lung cancer. Single-dose externalbeam radiation up-regulates CD70 in PC3 cells (Bernstein et al., 2014;Kumari and Garnett-Benson, 2016; Pu et al., 2014).

CDH3 (also known as P-cadherin) encodes cadherin 3 which is a classicalcadherin of the cadherin superfamily. This calcium-dependent cell-celladhesion protein is comprised of five extracellular cadherin repeats, atransmembrane region and a highly conserved cytoplasmic tail. This geneis located in a gene cluster in a region on the long arm of chromosome16 that is involved in loss of heterozygosity events in breast andprostate cancer. In addition, aberrant expression of this protein isobserved in cervical adenocarcinomas (RefSeq, 2002). CDH3 is involved inoncogenic signaling and activates integrins, receptor tyrosine kinases,small molecule GTPases, EMT transcription factors, and other cadherinfamily members. CDH3 signaling induces invasion and metastasis(Albergaria et al., 2011; Paredes et al., 2012; Bryan, 2015; Vieira andParedes, 2015). Oncogenic activation of CDH3 is involved in gastriccarcinogenesis (Resende et al., 2011). CDH3 over-expression promotesbreast cancer, bladder cancer, ovarian cancer, prostate cancer,endometrial cancer, skin cancer, gastric cancer, pancreas cancer, andcolon cancer (Albergaria et al., 2011; Paredes et al., 2007; Bryan andTselepis, 2010; Reyes et al., 2013; Vieira and Paredes, 2015). CDH3 is abasal epithelial marker expressed in basal-like breast cancer. BRCA1carcinomas are characterized by the expression of basal markers likeCDH3 and show a high-grade, highly proliferating, ER-negative, andHER3-negative phenotype (Honrado et al., 2006; Palacios et al., 2008;Rastelli et al., 2010; Dewar et al., 2011). CDH3 is a tumor suppressorin melanoma and oral squamous cell carcinoma (Haass et al., 2005; Vieiraand Paredes, 2015). CDH3 may be used as EMT marker. There is a shiftfrom E-cadherin to N-cadherin and CDH3 expression during tumor formationand progression (Piura et al., 2005; Bonitsis et al., 2006; Bryan andTselepis, 2010; Ribeiro and Paredes, 2014). Competitive interactionbetween CDH3 and beta-catenin causes impaired intercellular interactionsand metastases in gastric cancer (Moskvina and Mal'kov, 2010). CDH3 maybe an early marker of cancer formation in colon cancer (Alrawi et al.,2006). Dys-regulation of CDH3 is a marker for poor prognosis andincreased malignancy (Knudsen and Wheelock, 2005).

CDKN2A (also known as p16 and p16INK4a) encodes cyclin dependent kinaseinhibitor 2A which generates several transcript variants which differ intheir first exons. At least three alternatively spliced variantsencoding distinct proteins have been reported, two of which encodestructurally related isoforms known to function as inhibitors of CDK4kinase. The remaining transcript includes an alternate first exonlocated 20 Kb upstream of the remainder of the gene; this transcriptcontains an alternate open reading frame (ARF) that specifies a proteinwhich is structurally unrelated to the products of the other variants.This ARF product functions as a stabilizer of the tumor suppressorprotein p53 as it can interact with, and sequester, the E3ubiquitin-protein ligase MDM2, a protein responsible for the degradationof p53 (RefSeq, 2002). CDKN2A is mutated in pancreatic ductaladenocarcinoma, cutaneous malignant melanoma, vulvar squamous cellcarcinoma, and biliary tract cancer. Mutations may be inherited andincrease the risk for developing pancreatic cancer. CDKN2A is deleted inmalignant pleural mesothelioma. CDKN2A is down-regulated in bladdercancer (Clancy et al., 2016; Fabbri et al., 2017; Gan et al., 2016;Kleeff et al., 2016; Nabeshima et al., 2016; Pacholczyk et al., 2016;Petersen, 2016; Sohal et al., 2016; Tatarian and Winter, 2016). CDKN2Ais involved in cancer cell proliferation, tumorigenesis, metastasis, Wntsignaling, senescence, apoptosis, and DNA repair mechanism (Gupta etal., 2016; Ko et al., 2016; Low et al., 2016; Sedgwick andD'Souza-Schorey, 2016; Zhao et al., 2016). CDKN2A is a tumor suppressorgene which is down-regulated upon over-expression of the oncogenicprotein UHRF1. CDKN2A interacts with p53 to suppress breast cancer(Alhosin et al., 2016; Fry et al., 2017). CDKN2A promotorhyper-methylation is associated with increased risk for low-gradesquamous intra-epithelial lesion, high-grade squamous intra-epitheliallesion, and cervical cancer and with smoking habit. CDKN2A isepigenetically dysregulated during the development of hepatocellularcarcinoma and esophageal squamous cell carcinoma (Han et al., 2017; Khanet al., 2017; Ma et al., 2016a). CDKN2A may be used in the diagnosis ofcervical cancer and oropharyngeal squamous cell carcinoma (Mahajan,2016; Savone et al., 2016; Tjalma, 2017). CDKN2A expression is caused byHPV infection, a virus which is known to have oncogenic potential (Hoffet al., 2017; Lorincz, 2016).

CDKN2B (also known as p15) encodes cyclin dependent kinase inhibitor 2Bwhich lies adjacent to the tumor suppressor gene CDKN2A in a region thatis frequently mutated and deleted in a wide variety of tumors. This geneencodes a cyclin-dependent kinase inhibitor, which forms a complex withCDK4 or CDK6, and prevents the activation of the CDK kinases, thus theencoded protein functions as a cell growth regulator that controls cellcycle G1 progression. The expression of this gene was found to bedramatically induced by TGF beta, which suggested its role in the TGFbeta induced growth inhibition (RefSeq, 2002). CDKN2B is involved in theregulation of the cell cycle progression and the inhibition of cellproliferation (Hu and Zuckerman, 2014; Roy and Banerjee, 2015). CDKN2Bdeletion is associated with schistosomal-associated bladder cancer.Mutations in CDKN2B may be involved in inherited susceptibility to glialtumors. CDKN2B is altered in meningiomas and mutated innon-muscle-invasive urothelial carcinoma (Mawrin and Perry, 2010; Melin,2011; Pollard et al., 2010; Alentorn et al., 2013; Idbaih, 2011;Koonrungsesomboon et al., 2015). CDKN2B is hyper-methylated in acutemyeloid leukemia and pituitary adenomas. CDKN2B is aberrantly regulatedin cutaneous malignant melanoma (Bailey et al., 2010; Jiang et al.,2014; Popov and Gil, 2010; van den Hurk et al., 2012; Wolff and Bies,2013; Zhou et al., 2014). CDKN2B interacts with the tumor suppressor RBand is regulated by Miz-1 and TGF-beta (Zhou et al., 2014; Geyer, 2010;Moroy et al., 2011). CDKN2B is a tumor suppressor gene which is affectedby long non-coding RNAs. CDKN2B itself in association with AS1 is partof a long non-coding RNA (ANRIL) which may be involved in cancerdevelopment (Popov and Gil, 2010; Aguilo et al., 2016; Shi et al., 2013;Wanli and Ai, 2015).

CLDN6, also known as claudin 6, encodes a member of the claudin familywhich is a component of tight junction strands and an integral membraneprotein (RefSeq, 2002). CLDN6 expression was shown to be associated withlymph node metastasis and TNM stage in non-small cell lung cancer (Wanget al., 2015b). Furthermore, low expression of CLDN6 was shown to beassociated with significantly lower survival rates in patients withnon-small cell lung cancer (Wang et al., 2015b). Thus, low CLDN6expression is an independent prognostic biomarker that indicates worseprognosis in patients with non-small cell lung cancer (Wang et al.,2015b). CLDN6 was shown to be down-regulated in cervical carcinoma andgastric cancer (Zhang et al., 2015e; Lin et al., 2013b). CLDN6 was shownto be up-regulated in BRCA1-related breast cancer and ovarian papillaryserous carcinoma (Wang et al., 2013; Heerma van Voss et al., 2014).CLDN6 was described as a tumor suppressor for breast cancer (Zhang etal., 2015e). Gain of CLDN6 expression in the cervical carcinoma celllines HeLa and C33A was shown to suppress cell proliferation, colonyformation in vitro, and tumor growth in vivo, suggesting that CLDN6 mayfunction as a tumor suppressor in cervical carcinoma cells (Zhang etal., 2015e). CLDN6 may play a positive role in the invasion andmetastasis of ovarian cancer (Wang et al., 2013). CLDN6 was shown to beconsistently expressed in germ cell tumors and thus is a noveldiagnostic marker for primitive germ cell tumors (Ushiku et al., 2012).CLDN6 expression was shown to be positive in most tumors of an assessedset of atypical teratoid/rhabdoid tumors of the central nervous system,with strong CLDN6 positivity being a potential independent prognosticfactor for outcome of the disease (Dufour et al., 2012).

CT45A1, also known as CT45, encodes the cancer/testis antigen family 45member A1 protein and is located on chromosome Xq26.3 (RefSeq, 2002).CT45 genes were shown to be potential prognostic biomarkers andtherapeutic targets in epithelial ovarian cancer (Zhang et al., 2015d).The CT45A1protein which is usually only expressed in testicular germcells was shown to be also expressed in lung cancer, breast cancer andovarian cancer (Chen et al., 2009). CT45A1 was also shown to beassociated with poor prognosis and poor outcomes in multiple myeloma(Andrade et al., 2009). CT45A1 was described as gene up-regulatingepithelial-mesenchymal transition (EMT) and metastatic genes, promotingEMT and tumor dissemination. Furthermore, CT45A1 was described as beingimplicated in the initiation or maintenance of cancer stem-like cells,promoting tumorigenesis and malignant progression (Yang et al., 2015b).CT45A1 over-expression in a breast cancer model was shown to result inthe up-regulation of various oncogenic and metastatic genes,constitutively activated ERK and CREB signaling pathways and increasedtumorigenesis, invasion and metastasis. Silencing of CT45A1 was shown toreduce cancer cell migration and invasion. Thus, CT45A1 may function asa novel proto-oncogene and may be a target for anticancer drug discoveryand therapy (Shang et al., 2014).

CT45A2 encodes one of a cluster of several similar genes, which is amember of the cancer/testis family of antigens and is located onchromosome Xq26.3 (RefSeq, 2002). CT45A2 was shown to be a novel splicedMLL fusion partner in a pediatric patient with de novo bi-phenotypicacute leukemia and thus might be relevant for leukemogenesis (Cerveiraet al., 2010). The cancer/testis antigen family 45 was shown to befrequently expressed in both cancer cell lines and lung cancer specimens(Chen et al., 2005). CT45 genes were shown to be potential prognosticbiomarkers and therapeutic targets in epithelial ovarian cancer (Zhanget al., 2015d).

CT45A3 encodes the cancer/testis antigen family 45 member A3 protein andis located on chromosome Xq26.3 (RefSeq, 2002). The cancer/testisantigen family 45 was shown to be frequently expressed in both cancercell lines and lung cancer specimens (Chen et al., 2005). CT45 geneswere shown to be potential prognostic biomarkers and therapeutic targetsin epithelial ovarian cancer (Zhang et al., 2015d).

CT45A4 encodes the cancer/testis antigen family 45 member A4 protein andis located on chromosome Xq26.3 (RefSeq, 2002). The cancer/testisantigen family 45 was shown to be frequently expressed in both cancercell lines and lung cancer specimens (Chen et al., 2005). CT45 geneswere shown to be potential prognostic biomarkers and therapeutic targetsin epithelial ovarian cancer (Zhang et al., 2015d).

CT45A5 encodes the cancer/testis antigen family 45 member A5 and islocated on chromosome Xq26.3 (RefSeq, 2002). The cancer/testis antigenfamily 45 was shown to be frequently expressed in both cancer cell linesand lung cancer specimens (Chen et al., 2005). CT45 genes were shown tobe potential prognostic biomarkers and therapeutic targets in epithelialovarian cancer (Zhang et al., 2015d).

CT45A6 encodes the cancer/testis antigen family 45 member A6 protein andis located on chromosome Xq26.3 (RefSeq, 2002). The cancer/testisantigen family 45 was shown to be frequently expressed in both cancercell lines and lung cancer specimens (Chen et al., 2005). CT45 geneswere shown to be potential prognostic biomarkers and therapeutic targetsin epithelial ovarian cancer (Zhang et al., 2015d).

CTAG2 encodes cancer/testis antigen 2 which is an auto immunogenic tumorantigen that belongs to the ESO/LAGE family of cancer-testis antigens.This protein is expressed in a wide array of cancers including melanoma,breast cancer, bladder cancer and prostate cancer. This protein is alsoexpressed in normal testis tissue (RefSeq, 2002). CTAG2 is involved incancer cell migration and invasiveness (Maine et al., 2016). CTAG2expression is up-regulated by LSAMP resulting in reduced cellproliferation (Baroy et al., 2014). CTAG2 is expressed in liposarcoma,lung cancer, urothelial cancer, and colorectal cancer. CTAG2 isover-expressed in several entities including esophageal squamous cellcarcinoma (Kim et al., 2012; Dyrskjot et al., 2012; Hemminger et al.,2014; Forghanifard et al., 2011; McCormack et al., 2013; Shantha Kumaraet al., 2012). Engineered T cells against CTAG2 may be used in multiplemyeloma treatment. Autoantibodies against CTAG2 may be used in cancerdiagnosis. CTAG2 may be a target in immunotherapy. CTAG2 expression isassociated with shorter progression-free survival (van et al., 2011;Dyrskjot et al., 2012; Hudolin et al., 2013; Pollack et al., 2012;Rapoport et al., 2015; Wang et al., 2015a).

CYP2W1 encodes a member of the cytochrome P450 superfamily of enzymeswhich are monooxygenases catalyzing many reactions involved in drugmetabolism and in the synthesis of cholesterol, steroids and otherlipids (RefSeq, 2002). CYP2W1 is over-expressed in a variety of humancancers including hepatocellular, colorectal and gastric cancer. CYP2W1over-expression is associated with tumor progression and poor survival(Aung et al., 2006; Gomez et al., 2010; Zhang et al., 2014a). Due totumor-specific expression, CYP2W1 is an interesting drug target orenzymatic activator of pro-drugs during cancer therapy (Karlgren andIngelman-Sundberg, 2007; Nishida et al., 2010).

DPPA2 encodes developmental pluripotency associated 2 and is located onchromosome 3q13.13 (RefSeq, 2002). DPPA2 is over-expressed in gastriccancer, non-small cell lung cancer, epithelial ovarian cancer, andcolorectal cancer. DPPA2 is an oncogene up-regulated in severalentities. DPPA2 is reciprocally repressed in teratoma (Tung et al.,2013; Ghodsi et al., 2015; John et al., 2008; Raeisossadati et al.,2014; Shabestarian et al., 2015; Tchabo et al., 2009; Western et al.,2011). DPPA2 expression correlates with tumor invasion depth, stage,lymph node metastasis, and aggressiveness (Ghodsi et al., 2015;Raeisossadati et al., 2014; Shabestarian et al., 2015). DPPA2 isinvolved in the pathogenesis of non-small cell lung cancer (Watabe,2012). DPPA2 is differentially methylated in thyroid cancer(Rodriguez-Rodero et al., 2013).

ENTPD4 (UDPase) encodes ectonucleoside triphosphate diphosphohydrolase4, a member of the apyrase protein family and may play a role insalvaging nucleotides from lysosomes (RefSeq, 2002). UDPase activity isincreased in patients with ovarian cancer or testicular cancer anddecreased after chemotherapy (Papadopoulou-Boutis et al., 1985).

ESR1 encodes an estrogen receptor, a ligand-activated transcriptionfactor important for hormone binding, DNA binding and activation oftranscription, that is essential for sexual development and reproductivefunction (RefSeq, 2002). Mutations and single nucleotide polymorphismsof ESR1 are associated with risk for different cancer types includingliver, prostate, gallbladder and breast cancer. The up-regulation ofESR1 expression is connected with cell proliferation and tumor growthbut the overall survival of patients with ESR1 positive tumors is betterdue to the successfully therapy with selective estrogen receptormodulators (Sun et al., 2015; Hayashi et al., 2003; Bogush et al., 2009;Miyoshi et al., 2010; Xu et al., 2011; Yakimchuk et al., 2013; Fuqua etal., 2014). ESR1 signaling interferes with different pathwaysresponsible for cell transformation, growth and survival like theEGFR/IGFR, PI3K/Akt/mTOR, p53, HER2, NFkappaB and TGF-beta pathways(Frasor et al., 2015; Band and Laiho, 2011; Berger et al., 2013;Skandalis et al., 2014; Mehta and Tripathy, 2014; Ciruelos Gil, 2014).

ETV1 encodes ETS variant 1 which is a member of the ETS (E twenty-six)family of transcription factors. The ETS proteins regulate many targetgenes that modulate biological processes like cell growth, angiogenesis,migration, proliferation and differentiation (RefSeq, 2002). ETV1 isinvolved in epithelial-to-mesenchymal transition, DNA damage response,AR and PTEN signaling, cancer cell invasion, and metastasis. ETV1interacts with JMJD2A to promote prostate carcinoma formation and toincrease YAP1 expression affecting the Hippo signaling pathway (Mesquitaet al., 2015; Baty et al., 2015; Heeg et al., 2016; Higgins et al.,2015; Kim et al., 2016; Lunardi et al., 2015). ETV1 expression isdecreased in prostate cancer. ETV1 is over-expressed in pancreaticcancer, gastrointestinal stromal tumors, oligodendroglial tumors, andrenal cell carcinoma. ETV1 may be an oncogene in non-small cell lungcancer (Heeg et al., 2016; Gleize et al., 2015; Ta et al., 2016; Al etal., 2015; Hashimoto et al., 2017; Jang et al., 2015). Increased mRNAlevels of ETV1 in microvesicles of prostate cancer cell lines arecorrelated with prostate cancer progression (Lazaro-lbanez et al.,2017). ETV1 is an oncogene which interacts with the Ewing's sarcomabreakpoint protein EWS. ETV1 interacts with Sparc and Has2 which mediatein part cancer cell metastasis and desmoplastic stromal expansion (Heeget al., 2016; Kedage et al., 2016). ETV1 gene fusion products as well asETV1 promotor methylation status are diagnostically useful (Angulo etal., 2016; 2015; Kumar-Sinha et al., 2015; Linn et al., 2015).

ETV4 (also called E1AF or PEA3) encodes a member of the Ets oncogenefamily of transcription factors and is involved in the regulation ofmetastasis gene expression and in the induction ofdifferentiation-associated genes in embryonic stem cell (Akagi et al.,2015; Coutte et al., 1999; Ishida et al., 2006). ETV4 is over-expressedin different cancer entities including breast, lung, colorectal andgastric cancer and is associated with migration, invasion, metastasisand poor prognosis (Benz et al., 1997; Horiuchi et al., 2003; Yamamotoet al., 2004; Keld et al., 2011; Hiroumi et al., 2001). ETV4 isup-regulated by different pathways like ERK/MAPK, HER2, PI3K and Rasfollowing an induction of several targets including MMPs and IL-8(Maruta et al., 2009; Keld et al., 2010; Chen et al., 2011b; Aytes etal., 2013).

ETV5 encodes the ETS variant 5 protein and is located on chromosome 3q28(RefSeq, 2002). Pathways including ETV5 were described as being deeplyrelated to the epithelial to mesenchymal process in endometrial cancer(Colas et al., 2012). ETV5 was shown to interact with several signalingpathways such as cell-cycle progression and the TGF-beta signalingpathway in the OV90 ovarian cancer cell line, and ETV5 expression wasshown to be associated with the expression of the oncogenictranscription factor FOXM1 in ovarian cancer (Llaurado et al., 2012b).Furthermore, ETV5 was shown to be up-regulated in ovarian cancer. In thespheroid model, the inhibition and up-regulation of ETV5 effected cellproliferation, cell migration, cell adhesion to extracellular matrixcomponents, cell-cell adhesion and cell survival. Thus, ETV5 may play arole in ovarian cancer progression, cell dissemination and metastasis(Llaurado et al., 2012a). Chromosomal rearrangements of ETV5 among othermembers of the oncogenic PEA3 subfamily, were described to occur inprostate tumors and are thought to be one of the major driving forces inthe genesis of prostate cancer. Furthermore, ETV5 was also described asan oncoprotein which is implicated in melanomas, breast and some othertypes of cancer (Oh et al., 2012). ETV5 was suggested to have asignificant role in regulating matrix metalloproteinase 2 expression andtherefore resorption in human chondrosarcoma, and thus may be atargetable up-stream effector of the metastatic cascade in this cancer(Power et al., 2013).

EYA2 encodes EYA transcriptional coactivator and phosphatase 2, a memberof the eyes absent (EYA) family of proteins involved in eye development(RefSeq, 2002). EYA2 over-expression has been observed in several tumortypes such as epithelial ovarian tumor, prostate, breast cancer, urinarytract cancers, glioblastoma, lung adenocarcinoma, cervical cancer, colonand hematopoietic cancers (Bierkens et al., 2013; Zhang et al., 2005;Guo et al., 2009; Patrick et al., 2013; Kohrt et al., 2014). Studieshave revealed that EYA2 influences transcription of TGF beta pathwaymembers as well as phosphorylation of TGFBR2, implying a dual role ofEYA2 in the pancreas (Vincent et al., 2014).

FAM111B encodes the family with sequence similarity 111 member B, aprotein with a trypsin-like cysteine/serine peptidase domain in theC-terminus which leads, in case of a mutation, to mottled pigmentation,telangiectasia, epidermal atrophy, tendon contractures, and progressivepulmonary fibrosis (RefSeq, 2002). FAM111B was found to bedown-regulated during metformin and aspirin induced inhibition ofpancreatic cancer development (Yue et al., 2015).

FAM83H encodes family with sequence similarity 83 member H which playsan important role in the structural development and calcification oftooth enamel. Defects in this gene are a cause of amelogenesisimperfecta type 3 (A13) (RefSeq, 2002). The long non-coding RNAFAM83H-AS1 is involved in cell proliferation, migration, and invasionand regulates MET/EGFR signaling (Zhang et al., 2017). The longnon-coding RNA FAM83H-AS1 is over-expressed in lung cancer andcolorectal cancer. FAM83H is an oncogene over-expressed in severalentities including breast cancer and colorectal cancer (Zhang et al.,2017; Kuga et al., 2013; Snijders et al., 2017; Yang et al., 2016c; Yanget al., 2016b). Increased expression of long non-coding RNA FAM83H-AS1is associated with shorter overall survival. FAM83H-AS1 is associatedwith poor prognosis (Yang et al., 2016c; Yang et al., 2016b). FAM83H maybe involved in androgen independent prostate cancer (NaIla et al.,2016). FAM83H interacts with CK1alpha to form keratin filaments anddesmosomes (Kuga et al., 2016).

FBN2, also known as fibrillin 2, encodes a protein which is a componentof the connective tissue and may be involved in elastic fiber assembly(RefSeq, 2002). FBN2 was described as an extracellular matrix regulatoryprotein of TGF-beta signaling activity (Lilja-Maula et al., 2014).Hyper-methylation of FBN2 was described as an epigenetic biomarker forclear cell renal cell carcinoma and early detection of colorectal cancerand as being associated with poor prognosis by colorectal cancerpatients (Ricketts et al., 2014; Rasmussen et al., 2016; Yi et al.,2012). FBN2 was shown to be a candidate cell surface target enriched inmedulloblastoma which could be used for the development oftumor-specific probes for guided resection in medulloblastoma (Haeberleet al., 2012).

FOLR1 encodes the folate receptor 1, which binds folic acid and itsreduced derivatives, and transports 5-methyltetrahydrofolate into cells;FOLR1 is a secreted protein that either anchors to membranes via aglycosyl-phosphatidylinositol linkage or exists in a soluble form(RefSeq, 2002). Being a major part of the FOLR1/cSrc/ERK1/2/NFκB/p53pathway, which is required for the up-take of folic acid, FOLR1 is ableto regulate the proliferation of cancer cells such as breast, lung andcolon cancer (Kuo and Lee, 2016; Cheung et al., 2016). FOLR1 was foundto be widely expressed in epithelial ovarian cancer, where itsexpression increases with tumor stage and might represent a potentialtherapeutic target (Leung et al., 2016; Ponte et al., 2016; Moore etal., 2016; Hou et al., 2017; Notaro et al., 2016; Bergamini et al.,2016). Reducing FOLR1 expression during colorectal cancer therapy wasshown to increase the effectiveness of 5-fluorouracil treatment(Tsukihara et al., 2016). FOLR1 represents an ideal tumor-associatedmarker for immunotherapy for triple-negative breast cancer as well ascolon cancer (Liang et al., 2016; Song et al., 2016).

GPR64 encodes adhesion G protein-coupled receptor G2, a member of the Gprotein-coupled receptor family described as an epididymis-specifictransmembrane protein (RefSeq, 2002). In breast cancer cell lines,knockdown of GPR64 resulted in a strong reduction in cell adhesion aswell as in cell migration (Peeters et al., 2015).

HOXA10 encodes homebox A10. This gene is part of the A cluster onchromosome 7 and encodes a DNA-binding transcription factor that mayregulate gene expression, morphogenesis, and differentiation. Morespecifically, it may function in fertility, embryo viability, andregulation of hematopoietic lineage commitment. Read-throughtranscription exists between this gene and the downstream homeobox A9(HOXA9) gene (RefSeq, 2002). HOXA10 is a stem cell factor whoseexpression correlates with CD133 expression in glioma and may beinvolved in cancer progression. HOXA10 is involved in cancer cellproliferation, migration, invasion, and metastasis. HOXA10 is involvedin multidrug resistance by inducing P-gp and MRP1 expression. HOXA10promotes epithelial-to-mesenchymal transition. HOXA10 may be adownstream target of miR-218/PTEN/AKT/PI3K signaling. HOXA10 promotesexpression of the AML-associated transcription factor Prdm16. HOXA10 maymediate G1 cell cycle arrest in a p21-dependent manner. HOXA10 isinvolved in TGF-beta2/p38 MAPK signaling promoting cancer cell invasionin a MMP-3-dependent manner (Carrera et al., 2015; Cui et al., 2014;Emmrich et al., 2014; Han et al., 2015; Li et al., 2014a; Li et al.,2016a; Sun et al., 2016; Xiao et al., 2014; Yang et al., 2016a; Yi etal., 2016; Yu et al., 2014; Zhang et al., 2014b; Zhang et al., 2015b).HOXA10 is up-regulated in gastric cancer and acute myeloid leukemia.HOXA10 is differentially expressed in oral squamous cell carcinoma.HOXA10 is differentially methylated in non-serous ovarian carcinoma andglioblastoma (Carrera et al., 2015; Han et al., 2015; Kurscheid et al.,2015; Niskakoski et al., 2014; Oue et al., 2015; Shima et al., 2014).HOXA10 methylation status may be used in breast cancer diagnosis. HOXA10and CD44 co-expression is correlated with tumor size and patientsurvival in gastric cancer. HOXA10 and miR-196b co-expression iscorrelated with poor prognosis in gastric cancer (Han et al., 2015; Limet al., 2013; Uehiro et al., 2016). SGI-110 treatment hypo-methylateHOXA10 which sensitizes ovarian cancer cells for chemotherapy (Fang etal., 2014a).

HOXA9 encodes homebox protein A9. This gene is part of the A cluster onchromosome 7 and encodes a DNA-binding transcription factor which mayregulate gene expression, morphogenesis, and differentiation. A specifictranslocation event which causes a fusion between this gene and theNUP98 gene has been associated with myeloid leukemogenesis (RefSeq,2002). HOXA9 is expressed in acute myeloid leukemia and high expressionis associated with adverse prognosis. HOXA9 and MEIS1 co-expressioninduces AML. HOXA9 is down-regulated in cervical cancer. HOXA9 isfrequently methylated in endometrial cancer (Alvarado-Ruiz et al., 2016;Chen et al., 2015; Li et al., 2016b; Li et al., 2016e; Sykes et al.,2016). The gene fusion product NUP98-HOXA9 acts as oncogene (Abe et al.,2016; Sontakke et al., 2016). Response to cisplatin-based chemotherapyis linked to HOXA9 promotor methylation status. HOXA9, MEIS1, and MN1co-expression in leukemia make the cells sensitive to pharmacologicinhibition of DOT1L (Li et al., 2016c; Riedel et al., 2016; Xylinas etal., 2016). HOXA9 is a tumor suppressor whose expression may be used todiagnose cancer (Ma et al., 2016b). HOXA9 mediates leukemic stem cellself-renewal and HIF-2alpha deletion accelerates this process (Vukovicet al., 2015; Zhu et al., 2016).

HOXB9 encodes homebox B9 which is a member of the Abd-B homeobox familyand encodes a protein with a homeobox DNA-binding domain. It is includedin a cluster of homeobox B genes located on chromosome 17. The encodednuclear protein functions as a sequence-specific transcription factorthat is involved in cell proliferation and differentiation. Increasedexpression of this gene is associated with some cases of leukemia,prostate cancer and lung cancer (RefSeq, 2002). HOXB9 is involved inangiogenic pathways which are regulated by miR-192. HOXB9 is adownstream target of Wnt/beta-catenin signaling induced byN-acetylgalactosaminyltransferase resulting in metastasis. HOXB9 mayregulate mesenchymal-to-epithelial transition in gastric carcinoma andcolon adenocarcinoma and epithelial-to-mesenchymal transition in breastcancer and hepatocellular carcinoma in a TGF-beta1-dependent manner.HOXB9 is involved in cell proliferation, migration, and invasion.TGF-beta1 down-regulates HOXB9 in a Kindlin-2/PDAC-dependent manner(Chang et al., 2015b; Darda et al., 2015; Hoshino et al., 2014; Huang etal., 2014; Kwon et al., 2015; Seki et al., 2012; Sha et al., 2015; Wu etal., 2016; Zhan et al., 2014; Zhan et al., 2015; Zhussupova et al.,2014). HOXB9 is differentially expressed in PBRM1 mutated clear cellrenal cell carcinoma. HOXB9 is over-expressed in platinum-resistanthigh-grade serous ovarian cancer, breast cancer, glioma, colonadenocarcinoma, hepatocellular carcinoma, and head and neck squamouscell carcinoma. HOXB9 expression is decreased in gastric carcinoma.HOXB9 is mutated in leukemia (Menezes et al., 2014; Chang et al., 2015b;Darda et al., 2015; Zhan et al., 2014; Zhussupova et al., 2014; Fang etal., 2014b; Hayashida et al., 2010; Kelly et al., 2016; Sha et al.,2013; Shrestha et al., 2012; Wang et al., 2016b; Yuan et al., 2014).HOXB9 expression is regulated by E2F1 and FAT10 (Zhussupova et al.,2014; Yuan et al., 2014). HOXB9 expression is correlated with tumor sizein oral cancer. HOXB9 expression is associated with advanced clinicalstage in glioma. HOXB9 down-regulation is associated with decreasedpatient survival in gastric carcinoma (Fang et al., 2014b; Sha et al.,2013; Oliveira-Costa et al., 2015; Tomioka et al., 2010). HOXB9regulates bladder cancer progression (Zhang et al., 2016b). Longnon-coding RNA nc-HOXB9-205 is down-regulated in urothelial carcinoma ofthe bladder (Luo et al., 2014). BCAS3-HOXB9 gene fusion product isexpressed in breast cancer (Schulte et al., 2012).

HOXC10 encodes homeobox C10 which belongs to the homeobox family ofgenes. The homeobox genes encode a highly conserved family oftranscription factors that play an important role in morphogenesis inall multicellular organisms. This gene is one of several homeobox HOXCgenes located in a cluster on chromosome 12. The protein level iscontrolled during cell differentiation and proliferation, which mayindicate this protein has a role in origin activation (RefSeq, 2002).HOXC10 is involved in chemo resistance by suppressing apoptosis andup-regulating NF-kappaB and DNA damage repair. HOXC10 induces apoptosisand inhibits cell growth. HOXC10 may be involved in cervical cancerprogression and invasion (Pathiraja et al., 2014; Sadik et al., 2016;Zhai et al., 2007). HOXC10 is up-regulated in thyroid cancer, cervicalsquamous cell carcinoma, and breast cancer (Abba et al., 2007; Zhai etal., 2007; Ansari et al., 2012; Feng et al., 2015). HOXC10 expressioncorrelates with shorter recurrence-free and overall survival inER-negative breast cancer. HOXC10 expression is associated with advancedstage, poor pathologic stage, poor prognosis, cytokine-cytokine receptorinteraction, and chemokine signaling pathways in thyroid cancer (Sadiket al., 2016; Feng et al., 2015). HOXC10 is differentially methylated inoral squamous cell carcinoma and small B cell lymophoma (Marcinkiewiczand Gudas, 2014a; Marcinkiewicz and Gudas, 2014b; Rahmatpanah et al.,2006).

HOXC9 encodes homebox C9 which belongs to the homeobox family of genes.The homeobox genes encode a highly conserved family of transcriptionfactors that play an important role in morphogenesis in allmulticellular organisms. This gene is one of several homeobox HOXC geneslocated in a cluster on chromosome 12 (RefSeq, 2002). HOXC9 is involvedin cancer cell invasion and proliferation. HOXC9 knock-down results inreduced cell viability, migration, invasion, tumorigenicity, andincreased autophagy. HOXC9 is involved in chemo resistance in bladdercancer in a miR-193a-3p-dependent manner. HOXC9 is involved in retinoicacid signaling and is involved in cell growth and differentiation (Huret al., 2016; Kocak et al., 2013; Lv et al., 2015a; Mao et al., 2011;Simeone et al., 1991; Stornaiuolo et al., 1990; Xuan et al., 2016; Zhaet al., 2012). HOXC9 is differentially expressed in breast cancer, lungcancer, and neuroblastoma. HOXC9 is methylated in stage I non-small celllung cancer. HOXC9 is up-regulated in astrocytoma. HOXC9 is expressed inesophageal cancer and cervical cancer (Hur et al., 2016; Xuan et al.,2016; Gu et al., 2007; Lin et al., 2009; Lopez et al., 2006; Okamoto etal., 2007). HOXC9 may be transcriptionally repressed by Smad4 (Zhou etal., 2008). HOXC9 expression is inversely associated with disease-freesurvival and distant metastasis-free survival in breast cancer. HOXC9expression is associated with poor prognosis in glioblastoma (Hur etal., 2016; Xuan et al., 2016). HOXC9 inhibits DAPK1 resulting indisturbed autophagy induced by Beclin-1 (Xuan et al., 2016).

HOXD10 encodes homeobox D10 protein, which functions as asequence-specific transcription factor that is expressed in thedeveloping limb buds and is involved in differentiation and limbdevelopment (RefSeq, 2002). HOXD10 was identified as target gene ofmiR-10b, which is up-regulated in gastric cancer (GC) and may have a keyrole in GC pathogenesis and development (Ma et al., 2015; Wang et al.,2015c). HOXD10 was found to be up-regulated in neck squamous cellcarcinoma and urothelial cancer promoting cell proliferation andinvasion and may represent a new biomarker for ductal invasive breastcarcinoma (Sharpe et al., 2014; Vardhini et al., 2014; Heubach et al.,2015). However, HOXD10 also showed tumor-suppressive functions incholangiocellular carcinoma by inactivating the RHOC/AKT/MAPK pathwayand inducing G1 phase cell cycle arrest (Yang et al., 2015a). As part ofthe miR-224/HOXD10/p-PAK4/MMP-9 signaling pathway, HOXD10 is contributedto the regulation of cell migration and invasion and provides a new biotarget for hepatocellular carcinoma treatment (Li et al., 2014b).

HOXD9 encodes homeobox D9 which belongs to the homeobox family of genes.The homeobox genes encode a highly conserved family of transcriptionfactors that play an important role in morphogenesis in allmulticellular organisms. This gene is one of several homeobox HOXD geneslocated at 2q31-2q37 chromosome regions. Deletions that removed theentire HOXD gene cluster or 5′ end of this cluster have been associatedwith severe limb and genital abnormalities. The exact role of this genehas not been determined (RefSeq, 2002). HOXD9 is involved inepithelial-to-mesenchymal transition, cancer cell migration, invasion,and metastasis in a ZEB1-dependent manner. Over-expressed HOXD9increases anchorage-independent growth and reduces contact inhibition.HOXD9 is involved in growth arrest and neuronal differentiation.Depletion of HOXD9 results in decreased cell proliferation, cell cyclearrest, and induction of apoptosis (Zha et al., 2012; Lawrenson et al.,2015b; Lv et al., 2015b; Tabuse et al., 2011). HOXD9 is up-regulated inlung squamous carcinoma and invasive hepatocellular carcinoma. HOXD9 isexpressed in esophageal carcinoma, astrocytomas and glioblastomas. HOXD9is differentially expressed in cervical cancer (Bao et al., 2016; Gu etal., 2007; Lv et al., 2015b; Tabuse et al., 2011; Li et al., 2002; Liuet al., 2005). HOXD9 expression is induced by retinoic acid and Wntsignaling (Ishikawa and Ito, 2009). HOXD9 may be involved in cervicalcarcinogenesis (Lopez-Romero et al., 2015). HOXD9 hyper-methylation isassociated with poorer disease-free and overall survival in lymph nodemetastasis (Marzese et al., 2014). HOXD9 is hyper-methylated incholangiocarcinoma and melanoma brain metastasis (Marzese et al., 2014;Sriraksa et al., 2013). HOXD9 may be involved in mucinous ovariancarcinoma susceptibility (Kelemen et al., 2015). HOXD9 may be anoncogene (Wu et al., 2013).

HTR3A encodes a 5-hydroxytryptamine (serotonin) receptor belonging tothe ligand-gated ion channel receptor superfamily that causes fast,depolarizing responses in neurons after activation (RefSeq, 2002). HTR3A(also called 5-HT3) is de-regulated in several cancer types for examplea down-regulation in mantle cell lymphomas, a differential expression indiverse B cell tumors and a decreased expression in breast cancer celllines (Pai et al., 2009; Rinaldi et al., 2010; Ek et al., 2002).

IGF2BP1, also known as CRD-BP, encodes a member of the insulin-likegrowth factor 2 mRNA-binding protein family which functions by bindingto the mRNAs of certain genes and regulating their translation (RefSeq,2002). Two members of the IGF2 mRNA binding protein family, includingIGF2BP1 were described as bona fide oncofetal proteins which are de novosynthesized in various human cancers and which may be powerfulpost-transcriptional oncogenes enhancing tumor growth, drug-resistanceand metastasis (Lederer et al., 2014). Expression of IGF2BP1 wasreported to correlate with an overall poor prognosis and metastasis invarious human cancers (Lederer et al., 2014). Thus, IGF2BP1 wassuggested to be a powerful biomarker and candidate target for cancertherapy (Lederer et al., 2014). IGF2BP family members were described tobe highly associated with cancer metastasis and expression of oncogenicfactors such as KRAS, MYC and MDR1 (Bell et al., 2013). IGF2BP1 wasshown to interact with C-MYC and was found to be expressed in the vastmajority of colon and breast tumors and sarcomas as well as in benigntumors such as breast fibroadenomas and meningiomas (Ioannidis et al.,2003). IGF2BP1 was shown to be up-regulated in hepatocellular carcinomaand basal cell carcinoma (Noubissi et al., 2014; Zhang et al., 2015c).Up-regulation of IGF2BP1 and other genes was shown to be significantlyassociated with poor post-surgery prognosis in hepatocellular carcinoma(Zhang et al., 2015c). IGF2BP1 was shown to be a target of the tumorsuppressor miR-9 and miR-372 in hepatocellular carcinoma and in renalcell carcinoma, respectively (Huang et al., 2015; Zhang et al., 2015c).Loss of stromal IGF2BP1 was shown to promote a tumorigenicmicroenvironment in the colon, indicating that IGF2BP1 plays atumor-suppressive role in colon stromal cells (Hamilton et al., 2015).IGF2BP1 was shown to be associated with stage 4 tumors, decreasedpatient survival and MYCN gene amplification in neuroblastoma and maytherefore be a potential oncogene and an independent negative prognosticfactor in neuroblastoma (Bell et al., 2015). IGF2BP1 was described as adirect target of WNT/B-catenin signaling which regulates GLI1 expressionand activities in the development of basal cell carcinoma (Noubissi etal., 2014).

IGF2BP3 encodes insulin-like growth factor II mRNA binding protein 3, anoncofetal protein, which represses translation of insulin-like growthfactor II (RefSeq, 2002). Several studies have shown that IGF2BP3 actsin various important aspects of cell function, such as cellpolarization, migration, morphology, metabolism, proliferation anddifferentiation. In vitro studies have shown that IGF2BP3 promotes tumorcell proliferation, adhesion, and invasion. Furthermore, IGF2BP3 hasbeen shown to be associated with aggressive and advanced cancers (Bellet al., 2013; Gong et al., 2014). IGF2BP3 over-expression has beendescribed in numerous tumor types and correlated with poor prognosis,advanced tumor stage and metastasis, as for example in neuroblastoma,colorectal carcinoma, intrahepatic cholangiocarcinoma, hepatocellularcarcinoma, prostate cancer, and renal cell carcinoma (Bell et al., 2013;Findeis-Hosey and Xu, 2012; Hu et al., 2014; Szarvas et al., 2014; Jenget al., 2009; Chen et al., 2011a; Chen et al., 2013; Hoffmann et al.,2008; Lin et al., 2013a; Yuan et al., 2009).

IRF4 encodes the interferon regulatory factor 4, a transcription factorthat negatively regulates Toll-like-receptor (TLR) signaling inlymphocytes, what is central to the activation of innate and adaptiveimmune system (RefSeq, 2002). IRFA is considered to be a key regulatorof several steps in lymphoid, myeloid, and dendritic celldifferentiation and maturation and is characterized by varying withinthe hematopoietic system in a lineage and stage-specific way (Shaffer etal., 2009; Gualco et al., 2010). IRF4 plays a pivotal role in adaptiveimmunity, cell growth, differentiation and tumorigenesis of chronicmyeloid leukemia, primary central nervous system lymphoma, T-celllymphoma, HTLV-I-induced adult T cell leukemia and intravascular largeB-cell lymphoma (Mamane et al., 2002; Orwat and Batalis, 2012; Bisig etal., 2012; Ponzoni et al., 2014; Manzella et al., 2016). IRF4 is awell-known oncogene that is regulated by enhancer of zeste homolog 2(EZH2) in multiple myeloma (Alzrigat et al., 2016).

KLK14 encodes kallikrein related peptidase 14 which is a member of thekallikrein subfamily of serine proteases that have diverse physiologicalfunctions such as regulation of blood pressure and desquamation. Thealtered expression of this gene is implicated in the progression ofdifferent cancers including breast and prostate tumors. The encodedprotein is a precursor that is proteolytically processed to generate thefunctional enzyme. This gene is one of the fifteen kallikrein subfamilymembers located in a cluster on chromosome 19 (RefSeq, 2002). KLK14 isinvolved in cell proliferation via phosphorylation of ERK1/2/MAP kinaseand tumorigenesis. KLK14 induces PAR-2 signaling. KLK14 may be involvedin tumor progression, growth, invasion, and angiogenesis (Walker et al.,2014; Borgono et al., 2007; Chung et al., 2012a; Devetzi et al., 2013;Gratio et al., 2011; Sanchez et al., 2012; Zhang et al., 2012a). KLK14is down-regulated by miR-378/422a and androgen receptor signaling.Androgen receptor signaling up-regulates KLK14 expression in breastcancer (Paliouras and Diamandis, 2008b; Lose et al., 2012; Paliouras andDiamandis, 2007; Paliouras and Diamandis, 2008a; Samaan et al., 2014).KLK14 is over-expressed in chronic lymphocytic leukemia, non-small celllung cancer, salivary gland tumors, and ovarian cancer. KLK14 isdifferentially expressed in breast cancer (Planque et al., 2008b;Fritzsche et al., 2006; Hashem et al., 2010; Kontos et al., 2016;Papachristopoulou et al., 2013; Planque et al., 2008a). KLK14 expressionis inversely associated with overall survival. KLK14 expression may beused as biomarker and to predict risk of disease recurrence. KLK14expression correlates with clinical tumor stage and positive nodalstatus (Devetzi et al., 2013; Lose et al., 2012; Fritzsche et al., 2006;Kontos et al., 2016; Borgono et al., 2003; Obiezu and Diamandis, 2005;Rabien et al., 2008; Rajapakse and Takahashi, 2007; Talieri et al.,2009).

KLK8 encodes the kallikrein related peptidase 8, a serine protease thatmay be involved in proteolytic cascade in the skin and may serve as abiomarker for ovarian cancer (RefSeq, 2002). KLK8 expression was shownto correlate with the progression of breast cancer colorectal cancer(CRC), endometrial carcinoma and ovarian cancer and might represent apotential independent prognostic indicator for colorectal, breast andovarian cancer (Liu et al., 2017; Jin et al., 2006; Kountourakis et al.,2009; Darling et al., 2008; Michaelidou et al., 2015; Borgono et al.,2006). KLK8 is able to undergo alternative splicing that generates anmRNA transcript missing exon 4; this alternative variant is, in contrastto KLK8, significantly down-regulated in cancer cells (Angelopoulou andKaragiannis, 2010). Nevertheless, the KLK8-T4 alternative splicevariant, alone or in combination, may be a new independent marker ofunfavorable prognosis in lung cancer (Planque et al., 2010). KLK8expression confers a favorable clinical outcome in non-small cell lungcancer by suppressing tumor cell invasiveness (Sher et al., 2006).

LAMA1 encodes an alpha 1 subunit of laminin an extracellular matrixglycoprotein with heterotrimeric structure, which constitute a majorcomponent of the basement membrane (RefSeq, 2002). LAMA1 is de-regulatedin different cancer types including up-regulation in glioblastomas,hyper-methylation in colorectal cancer, abnormal methylation in breastcancer and frameshift mutations in gastric cancer (Scrideli et al.,2008; Choi et al., 2015; Simonova et al., 2015; Kim et al., 2011).TGFbeta can induce the expression of LAMA1. LAMA1 in turn promotescollagenase IV production, which leads to an invasive phenotype inbenign tumor cells, but is not sufficient to confer metastatic potential(Chakrabarty et al., 2001; Royce et al., 1992).

LAMC2 belongs to the family of laminins, a family of extracellularmatrix glycoproteins. Laminins are the major non-collagenous constituentof basement membranes. They have been implicated in a wide variety ofbiological processes including cell adhesion, differentiation,migration, signaling, neurite outgrowth and metastasis. LAMC2 encodes aprotein which is expressed in several fetal tissues and is specificallylocalized to epithelial cells in skin, lung and kidney (RefSeq, 2002).LAMC2 is highly expressed in anaplastic thyroid carcinoma and isassociated with tumor progression, migration, and invasion by modulatingsignaling of EGFR (Garg et al., 2014). LAMC2 expression predicted poorerprognosis in stage II colorectal cancer patients (Kevans et al., 2011).LAMC2 expression together with three other biomarkers was found to besignificantly associated with the presence of LN metastasis in oralsquamous cell carcinoma patients (Zanaruddin et al., 2013).

LILRB4 (also known as ILT-3) encodes leukocyte immunoglobulin likereceptor B4 which is a member of the leukocyte immunoglobulin-likereceptor (LIR) family, which is found in a gene cluster at chromosomalregion 19q13.4. The receptor is expressed on immune cells where it bindsto MHC class I molecules on antigen-presenting cells and transduces anegative signal that inhibits stimulation of an immune response. Thereceptor can also function in antigen capture and presentation. It isthought to control inflammatory responses and cytotoxicity to help focusthe immune response and limit autoreactivity (RefSeq, 2002).Over-expression of LILRB4 may be involved in tolerance of dendriticcells during cancer. LILRB4 may be involved in immune suppression.LILRB4 is involved in cancer immune escape (Zhang et al., 2012b;Trojandt et al., 2016; Cortesini, 2007; de Goeje et al., 2015;Suciu-Foca et al., 2007). LILRB4 expression is induced by TNF-alpha.Over-expression of LILRB4 inhibits NF-kappaB activation, transcriptionof inflammatory cytokines, and co-stimulatory molecules. LILRB4 isover-expressed by cyclosporine resulting in decreased tumor cytotoxicityby natural killer cells (Si et al., 2012; Thorne et al., 2015; Vlad andSuciu-Foca, 2012). LILRB4 is over-expressed on dendritic cells incancer. LILRB4 is expressed in monocytic acute myeloid leukemia. LILRB4is over-expressed in ovarian cancer (Dobrowolska et al., 2013; Khan etal., 2012; Orsini et al., 2014). LILRB4 expression is associated withshorter survival in non-small cell lung cancer. LILRB4 expression may beused in chronic lymphocytic leukemia prognosis (Colovai et al., 2007; deGoeje et al., 2015).

LOXL2 encodes an extracellular copper-dependent amine oxidase, known aslysyl oxidase like 2. The enzyme is essential to the biogenesis ofconnective tissue and catalyses the first step in the formation ofcrosslinks between collagens and elastin (RefSeq, 2002). LOXL2 was shownto be involved in regulation of extracellular and intracellular cellsignaling pathways. Extracellularly, LOXL2 remodels the extracellularmatrix of the tumor microenvironment. Intracellularly, it regulates theepithelial-to-mesenchymal transition (Cano et al., 2012; Moon et al.,2014). In general, LOXL2 has been associated with tumor progressionincluding the promotion of cancer cell invasion, metastasis,angiogenesis, and the malignant transformation of solid tumors invarious tumors. A high expression of LOXL2 is associated with a poorprognosis (Wu and Zhu, 2015). LOXL2 was shown to be overexpressed incolon, esophageal squamous cell, breast cell, clear cell renal cell,hepatocellular, cholangio-, lung squamous cell and head and necksquamous cell carcinomas. In various cancer types, the high expressionof LOXL2 was associated with higher recurrence, progression, ormetastasis. In various cancer cell lines, the high expression of LOXL2was associated with increased cell mobility and invasion and itssilencing showed the opposite effects (Xu et al., 2014a; Kim et al.,2014; Wong et al., 2014a; Hase et al., 2014; Lv et al., 2014; Torres etal., 2015). In gastric cancer, fibroblast-derived LOXL2 was shownpotentially to stimulate the motility of gastric cancer cells. Theexpression of LOXL2 in stromal cells could serve as a prognostic marker(Kasashima et al., 2014). A number of micro RNAs family is significantlyreduced in cancer tissues. LOXL2 was shown to be a direct regulator ofthose tumor-suppressive micro-RNAs (Fukumoto et al., 2016; Mizuno etal., 2016).

EGF induces LRRK1 translocation as it is an EGF receptor specificinteraction partner (Ishikawa et al., 2012; Hanafusa and Matsumoto,2011; Reyniers et al., 2014). LRRK1 is a component of the Grb2/Gab2/Shc1complex and interacts with Arap1. It may be a component of the MAPKsignaling in response to cellular stress (Titz et al., 2010). Arsenictrioxide which is used for acute promyelocytic leukemia treatmentup-regulates LRRK1 in breast cancer cells (Wang et al., 2011). LRRK1shows extreme allele-specific expression in familial pancreatic cancer(Tan et al., 2008). LRRK1 encodes leucine rich repeat kinase 1 and islocated on chromosome 15q26.3. It belongs to the ROCO proteins, a novelsubgroup of Ras-like GTPases (RefSeq, 2002; Korr et al., 2006).

LYPD1 encodes LY6/PLAUR domain containing 1 and is located on chromosome2q21.2 (RefSeq, 2002). LYPD1 is over-expressed in brain metastasesderived from breast cancer. LYPD1 is over-expressed in metastasis. LYPD1is differentially expressed in ovarian cancer. LYPD1 is a tumorsuppressor which is down-regulated in CD133+ cancer stem cell-like cellsderived from uterine carcinosarcoma (Burnett et al., 2015; Choijamts etal., 2011; Dat et al., 2012; Ge et al., 2015b; Lawrenson et al., 2015a).LYPD1 is a negative regulator of cell proliferation (Salazar et al.,2011).

MAGEA11 encodes MAGE family member A11 which is a member of the MAGEAgene family. The members of this family encode proteins with 50 to 80%sequence identity to each other. The promoters and first exons of theMAGEA genes show considerable variability, suggesting that the existenceof this gene family enables the same function to be expressed underdifferent transcriptional controls. The MAGEA genes are clustered atchromosomal location Xq28 (RefSeq, 2002). MAGEA11 is a cancer germlineantigen which is involved in tumor progression and correlates with poorprognosis and survival in silico. MAGEA11 is involved in PR-B signalingand acts as co-regulator for the androgen receptor. MAGEA11 directlyinteracts with TIF2. MAGEA11 is involved in hypoxic signaling andknock-down leads to decreased HIF-1alpha expression (Aprelikova et al.,2009; Askew et al., 2009; James et al., 2013; Liu et al., 2011; Su etal., 2012; Wilson, 2010; Wilson, 2011). MAGEA11 is up-regulated in oralsquamous cell carcinoma, paclitaxel-resistant ovarian cancer, and duringprostate cancer progression (Duan et al., 2003; Wilson, 2010; Ge et al.,2015a; Karpf et al., 2009). MAGEA11 expression is associated withhypo-methylation in prostate and epithelial ovarian cancer (James etal., 2013).

MAGEA12 encodes MAGE family member A12 and is closely related to severalother genes clustered on chromosome X (RefSeq, 2002). MAGEA12 isexpressed in 20.5% of multiple myeloma patients (Andrade et al., 2008).The surfacing of systemic immune reactivity toward a cryptic epitopefrom the MAGEA12, after temporary regression of a single melanomametastasis, in response to specific vaccination was reported (Lally etal., 2001). MAGEA12 was expressed at the highest frequencies, relativeto the other MAGE antigens, in early stage lesions of malignant melanoma(Gibbs et al., 2000).

MAGEA3 encodes melanoma-associated antigen family member A3. MAGEA3 iswidely known as cancer-testis antigen (RefSeq, 2002; Pineda et al.,2015; De et al., 1994). MAGEA3 has been known long time for being usedin therapeutic vaccination trials of metastatic melanoma cancer. Thecurrently performed percutaneous peptide immunization with MAGEA3 and 4other antigens of patients with advanced malignant melanoma was shown tocontribute significantly to longer overall survival by completeresponders compared to incomplete responders (Coulie et al., 2002;Fujiyama et al., 2014). In NSCLC, MAGEA3 was shown to be frequentlyexpressed. The expression of MAGEA3 correlated with higher number oftumor necrosis in NSCLC tissue samples and was shown to inhibit theproliferation and invasion and promote the apoptosis in lung cancer cellline. By the patients with adenocarcinomas, the expression of MAGEA3 wasassociated with better survival. The whole cell anti MAGEA3 vaccine iscurrently under the investigation in the promising phase III clinicaltrial for treatment of NSCLC (Perez et al., 2011; Reck, 2012; Hall etal., 2013; Grah et al., 2014; Liu et al., 2015b). MAGEA3 together with 4other genes was shown to be frequently expressed in HCC. The expressionof those genes was correlated with the number of circulating tumorcells, high tumor grade and advanced stage in HCC patients. Thefrequency of liver metastasis was shown to be significantly higher incases with tumor samples that expressed MAGE3 than in those that did notexpress this gene (Bahnassy et al., 2014; Hasegawa et al., 1998). Cancerstem cell-like side populations isolated from a bladder cancer cell lineas well as from lung, colon, or breast cancer cell lines showedexpression of MAGEA3 among other cancer-testis antigens. In general,cancer stem cells are known for being resistant to current cancertherapy and cause post-therapeutic cancer recurrence and progression.Thus, MAGEA3 may serve as a novel target for immunotherapeutic treatmentin particular of bladder cancer (Yamada et al., 2013; Yin et al., 2014).In head and neck squamous cell carcinoma, the expression of MAGEA3 wasshown to be associated with better disease-free survival (Zamuner etal., 2015). Furthermore, MAGEA3 can be used as a prognostic marker forovarian cancer (Szajnik et al., 2013).

MAGEA4, also known as MAGE4, encodes a member of the MAGEA gene familyand is located on chromosome Xq28 (RefSeq, 2002). MAGEA4 was describedas a cancer testis antigen which was found to be expressed in a smallfraction of classic seminomas but not in non-seminomatous testiculargerm cell tumors, in breast carcinoma, Epstein-Barr Virus-negative casesof Hodgkin's lymphoma, esophageal carcinoma, lung carcinoma, bladdercarcinoma, head and neck carcinoma, and colorectal cancer, oral squamouscell carcinoma, and hepatocellular carcinoma (Ries et al., 2005; Bode etal., 2014; Li et al., 2005; Ottaviani et al., 2006; Hennard et al.,2006; Chen et al., 2003). MAGEA4 was shown to be frequently expressed inprimary mucosal melanomas of the head and neck and thus may be apotential target for cancer testis antigen-based immunotherapy (Prasadet al., 2004). MAGEA4 was shown to be preferentially expressed in cancerstem-like cells derived from LHK2 lung adenocarcinoma cells, SW480 colonadenocarcinoma cells and MCF7 breast adenocarcinoma cells (Yamada etal., 2013). Over-expression of MAGEA4 in spontaneously transformednormal oral keratinocytes was shown to promote growth by preventing cellcycle arrest and by inhibiting apoptosis mediated by the p53transcriptional targets BAX and CDKN1A (Bhan et al., 2012). MAGEA4 wasshown to be more frequently expressed in hepatitis C virus-infectedpatients with cirrhosis and late-stage hepatocellular carcinoma comparedto patients with early stage hepatocellular carcinoma, thus making thedetection of MAGEA4 transcripts potentially helpful to predict prognosis(Hussein et al., 2012). MAGEA4 was shown to be one of severalcancer/testis antigens that are expressed in lung cancer and which mayfunction as potential candidates in lung cancer patients for polyvalentimmunotherapy (Kim et al., 2012). MAGEA4 was described as beingup-regulated in esophageal carcinoma and hepatocellular carcinoma (Zhaoet al., 2002; Wu et al., 2011). A MAGEA4-derived native peptide analoguecalled p286-1Y2L9L was described as a novel candidate epitope suitableto develop peptide vaccines against esophageal cancer (Wu et al., 2011).

MAGEA6 encodes melanoma-associated antigen family member A6. MAGEA3 iswidely known as cancer-testis antigen (RefSeq, 2002; Pineda et al.,2015; De et al., 1994). MAGEA6 was shown to be frequently expressed inmelanoma, advanced myeloma, pediatric rhabdomyosarcoma, sarcoma, lung,bladder, prostate, breast, and colorectal cancers, head and necksquamous cell, esophageal squamous cell, and oral squamous cellcarcinomas (Ries et al., 2005; Hasegawa et al., 1998; Gibbs et al.,2000; Dalerba et al., 2001; Otte et al., 2001; van der Bruggen et al.,2002; Lin et al., 2004; Tanaka et al., 1997). MAGEA6 expression has beenassociated with shorter progression-free survival in multiple myelomapatients. In contrast in head and neck squamous cell carcinoma, theexpression of MAGEA6 was shown to be associated with better disease-freesurvival (van et al., 2011; Zamuner et al., 2015). MAGEA6 was among aset of genes overexpressed in a paclitaxel-resistant ovarian cancer cellline. Moreover, transfection of MAGEA6 also conferred increased drugresistance to paclitaxel-sensitive cells (Duan et al., 2003). MAGEA6 canbe used as a prognostic marker for ovarian cancer (Szajnik et al.,2013). Cancer stem cell-like side populations isolated from lung, colon,or breast cancer cell lines showed expression of MAGEA6 among othercancer-testis antigens (Yamada et al., 2013).

MAGEB2 is classified as cancer testis antigen, since it is expressed intestis and placenta, and in a significant fraction of tumors of varioushistological types, amongst others multiple myeloma and head and necksquamous cell carcinoma (Pattani et al., 2012; van et al., 2011).

MELK encodes maternal embryonic leucine zipper kinase and is located onchromosome 9p13.2 (RefSeq, 2002). MELK is a member of the SNF1/AMPKfamily of serine-threonine kinases and is a cell cycle dependent proteinkinase. It plays a key role in multiple cellular processes such as theproliferation, cell cycle progression, mitosis and spliceosome assemblyand has recently emerged as an oncogene and a biomarker over-expressedin multiple cancer stem cells (Du et al., 2014). MELK is over-expressedin various cancers, including colon, gastric, breast, ovaries, pancreas,prostate and brain cancer and over-expression correlates with poorprognosis (Pickard et al., 2009; Kuner et al., 2013; Gu et al., 2013;Liu et al., 2015a). Inhibition of MELK is under investigation as atherapeutic strategy for a variety of cancers, including breast cancer,lung cancer and prostate cancer. MELK-T1 inhibits catalytic activity andMELK protein stability and might sensitize tumors to DNA-damaging agentsor radiation therapy by lowering the DNA-damage threshold. MELKinhibitor OTSSP167 is undergoing phase I clinical trials (Chung et al.,2012b; Ganguly et al., 2014; Beke et al., 2015).

MEX3A encodes a member of the mex-3 RNA binding family which consists ofevolutionarily conserved RNA-binding proteins recruited to P bodies andpotentially involved in post-transcriptional regulatory mechanisms(Buchet-Poyau et al., 2007). MEX3A is over-expressed and the gene isamplified in Wilms tumors associated with a late relapse (Krepischi etal., 2016). MEX3A regulates CDX2 via a post-transcriptional mechanismwith impact in intestinal differentiation, polarity and stemness,contributing to intestinal homeostasis and carcinogeneses (Pereira etal., 2013).

MMP-11, also named stromelysin-3, is a member of the stromelysinsubgroup belonging to MMPs superfamily, which has been detected incancer cells, stromal cells and adjacent microenvironment. Differently,MMP-11 exerts a dual effect on tumors. On the one hand MMP-11 promotescancer development by inhibiting apoptosis as well as enhancingmigration and invasion of cancer cells, on the other hand MMP-11 plays anegative role against cancer development via suppressing metastasis inanimal models. Overexpression of MMP-11 was discovered in sera of cancerpatients compared with normal control group as well as in multiple tumortissue specimens, such as gastric cancer, breast cancer, and pancreaticcancer (Zhang et al., 2016c). MMP-11 was demonstrated to beover-expressed at mRNA level and protein level in CRC tissue than pairednormal mucosa. Further MMP-11 expression was correlated with CRC lymphnode metastasis, distant metastasis and TNM stage (Tian et al., 2015).MMP-11 overexpression is associated with aggressive tumor phenotype andunfavorable clinical outcome in upper urinary tract urothelialcarcinomas (UTUC) and urinary bladder urothelial carcinomas (UBUC),suggesting it may serve as a novel prognostic and therapeutic target (Liet al., 2016d).

MMP12 (also called MME) encodes a member of the matrix metalloproteinasefamily which is involved in the breakdown of extracellular matrix innormal physiological processes, such as embryonic development,reproduction and tissue remodeling as well as in disease processes, suchas arthritis and metastasis (RefSeq, 2002). De-regulation of MMP12 isshown for different cancer entities. MMP12 is up-regulated in lung,skin, pancreatic and gastric cancer and related to tumor invasion andmetastasis. In contrast, over-expression of MMP12 mRNA was found ingastric and colorectal cancer and correlated with a better prognosis(Zhang et al., 2007; Yang et al., 2001; Balaz et al., 2002; Zheng etal., 2013; Wen and Cai, 2014; Zhang et al., 2015f). MMP12 isup-regulated by TNF-alpha or EGF via the NF-kappaB/MAPK and JNK/AP-1pathways (Yu et al., 2010; Yang et al., 2012).

MYO3B encodes the myosin IIIB, a member of a myosin-class that ischaracterized by an amino-terminal kinase domain and shown to be presentin photoreceptors (RefSeq, 2002). MYO3B was identified as an antagonistto trastuzumab treatment among HER2+ cell lines (Lapin et al., 2014).Nucleotide polymorphisms in the MYOB3 gene were found to be associatedwith changes in the AUA Symptom Score after radiotherapy for prostatecancer (Kerns et al., 2013).

NFE2L3 encodes nuclear factor, erythroid 2 like 3, a member of the cap‘n’ collar basic-region leucine zipper family of transcription factors(RefSeq, 2002). Recent work has revealed that loss of NFE2L3 predisposesmice to lymphoma development. Others have observed high levels of NFE2L3in colorectal cancer cells, whereas aberrant expression of NFE2L3 wasfound in Hodgkin lymphoma. Furthermore, NFE2L3 exhibitedhyper-methylation in ER positive tumors (Kuppers et al., 2003;Chevillard et al., 2011; Palma et al., 2012; Rauscher et al., 2015).

NLRP2 (also known as NALP2) encodes the NLR family, pyrin domaincontaining 2 protein and is involved in the activation of caspase-1 andmay also form protein complexes activating proinflammatory caspases.NLRP7 is a paralog of NLRP2 (RefSeq, 2002; Wu et al., 2010; Slim et al.,2012). The PYRIN domain of NLRP2 inhibits cell proliferation and tumorgrowth of glioblastoma (Wu et al., 2010). An ATM/NLRP2/MDC1-dependentpathway may shut down ribosomal gene transcription in response tochromosome breaks (Kruhlak et al., 2007). Mutations in NLRP2 can causerare human imprinting disorders such as familial hydatidiform mole,Beckwith-Wiedemann syndrome and familial transient neonatal diabetesmellitus (Aghajanova et al., 2015; Dias and Maher, 2013; Ulker et al.,2013). NLRP2 inhibits NF-kappaB activation (Kinoshita et al., 2005;Kinoshita et al., 2006; Fontalba et al., 2007; Bruey et al., 2004).

NLRP7 encodes the NLR family pyrin domain containing 7, a member of theNACHT, leucine rich repeat, and PYD containing (NLRP) protein familythat may act as a feedback regulator of caspase-1-dependent interleukin1-beta secretion (RefSeq, 2002). NLRP7 expression correlatessignificantly with the depth of tumor invasion and poor prognosis inendometrial cancer and was identified as one of the genes highlyexpressed in embryonal carcinomas (Ohno et al., 2008; Skotheim et al.,2005). NLRP7 might play a crucial role in cell proliferation intesticular tumorigenesis and represents a promising therapeutic targetfor testicular germ cell tumors (Okada et al., 2004).

OVGP1 or oviduct-specific glycoprotein, encodes a large,carbohydrate-rich, epithelial glycoprotein which is secreted fromnon-ciliated oviductal epithelial cells and associates with ovulatedoocytes, blastomeres and spermatozoan acrosomal regions (RefSeq, 2002).Gain of OVGP1 was shown to be associated with the development ofendometrial hyperplasia and endometrial cancer (Woo et al., 2004). OVGP1was described as a molecular marker for invasion in endometrialtumorigenesis and a differentiation-based marker of different ovariancancers (Maines-Bandiera et al., 2010; Wang et al., 2009).

PAGE2 encodes a member of the PAGE protein family, which ispredominantly expressed in testis (Brinkmann et al., 1998). Thecancer-testis gene PAGE2 is up-regulated by de-methylation duringspontaneous differentiation of colorectal cancer cells resulting inmesenchymal-to-epithelial transition (MET). Accordingly, down-regulationof PAGE2 has been shown in EMT (Yilmaz-Ozcan et al., 2014). Agenome-wide screening identifies PAGE2 as a possible regulator oftelomere signaling in human cells (Lee et al., 2011).

PNOC encodes prepronociceptin which is a preproprotein that isproteolytically processed to generate multiple protein products. Theseproducts include nociceptin, nocistatin, and orphanin FQ2 (OFQ2).Nociceptin, also known as orphanin FQ, is a 17-amino acid neuropeptidethat binds to the nociceptin receptor to induce increased painsensitivity, and may additionally regulate body temperature, learningand memory, and hunger.

Another product of the encoded preproprotein, nocistatin, may inhibitthe effects of nociception (RefSeq, 2002). Inhibition of cancer painalso inhibits tumor growth and lung metastasis. PNOC is involved inmorphine tolerance development. PNOC is involved in neuronal growth.PNOC is involved in cell damage, viability, inflammation and impairedimmune function (Caputi et al., 2013; Chan et al., 2012; Kirkova et al.,2009; Kuraishi, 2014; Stamer et al., 2011). PNOC is up-regulated inganglioglioma. PNOC expression is down-regulated in end-stage cancer.PNOC is highly expressed in the plasma of hepatocellular carcinomapatients (Chan et al., 2012; Stamer et al., 2011; Horvath et al., 2004;Spadaro et al., 2006; Szalay et al., 2004). Cebranopadol is an analgesicPNOC peptide may be used in bone cancer treatment and buprenorphine inlung cancer treatment (Davis, 2012; Linz et al., 2014). PNOC is involvedin c-Fos expression (Gottlieb et al., 2007; Kazi et al., 2007).

PRAME encodes an antigen that is preferentially expressed in humanmelanomas and acts as a repressor of retinoic acid receptor, likelyconferring a growth advantage to cancer cell via this function (RefSeq,2002). PRAME was shown to be up-regulated in multiple myeloma, clearcell renal cell carcinoma, breast cancer, acute myeloid leukemia,melanoma, chronic myeloid leukemia, head and neck squamous cellcarcinoma and osteosarcoma cell lines (Dannenmann et al., 2013; Yao etal., 2014; Zou et al., 2012; Szczepanski and Whiteside, 2013; Zhang etal., 2013; Beard et al., 2013; Abdelmalak et al., 2014; Qin et al.,2014). PRAME is associated with myxoid and round-cell liposarcoma(Hemminger et al., 2014). PRAME is associated with shorterprogression-free survival and chemotherapeutic response in diffuse largeB-cell lymphoma treated with R-CHOP, markers of poor prognosis in headand neck squamous cell carcinoma, poor response to chemotherapy inurothelial carcinoma and poor prognosis and lung metastasis inosteosarcoma (Tan et al., 2012; Dyrskjot et al., 2012; Szczepanski etal., 2013; Mitsuhashi et al., 2014). PRAME is associated with lowerrelapse, lower mortality and overall survival in acute lymphoblasticleukemia (Abdelmalak et al., 2014). PRAME may be a prognostic marker fordiffuse large B-cell lymphoma treated with R-CHOP therapy (Mitsuhashi etal., 2014).

RAD54 encodes a protein belonging to the DEAD-like helicase superfamily.It shares similarity with Saccharomyces cerevisiae RAD54 and RDH54, bothof which are involved in homologous recombination and repair of DNA.This protein binds to double-stranded DNA, and displays ATPase activityin the presence of DNA. This gene is highly expressed in testis andspleen, which suggests active roles in meiotic and mitotic recombination(RefSeq, 2002). Homozygous mutations of RAD54B were observed in primarylymphoma and colon cancer (Hiramoto et al., 1999). RAD54B counteractsgenome-destabilizing effects of direct binding of RAD51 to dsDNA inhuman tumor cells (Mason et al., 2015).

RNF17 encodes ring finger protein 17 which is similar to a mouse genethat encodes a testis-specific protein containing a RING finger domain.Alternatively spliced transcript variants encoding different isoformshave been found (RefSeq, 2002). RNF17 is involved in cytokine productionand apoptosis. RNF17 enhances c-Myc function (Jnawali et al., 2014; Leeet al., 2013; Yin et al., 1999; Yin et al., 2001). RNF17 is up-regulatedupon RHOXF1 knock-down (Seifi-Alan et al., 2014). RNF17 is expressed inliver cancer (Yoon et al., 2011). RNF17 is a cancer-associated marker(de Matos et al., 2015).

SDK2 encodes the sidekick cell adhesion molecule 2, a member of theimmunoglobulin superfamily that contains two immunoglobulin domains andthirteen fibronectin type III domains which represent binding sites forDNA, heparin and the cell surface (RefSeq, 2002). It was shown that SDK2guides axonal terminals to specific synapses in developing neurons andpromotes lamina-specific targeting of retinal dendrites in the innerplexiform layer (Kaufman et al., 2004; Yamagata and Sanes, 2012).

SPDEF (also called PDEF) encodes SAM pointed domain containing ETStranscription factor, a member of the E26 transformation-specific (ETS)family of transcription factors. It is highly expressed in prostateepithelial cells where it functions as an androgen-independenttransactivator of prostate specific antigen (PSA) promoter (RefSeq,2002). SPDEF expression is often lost or down-regulated in late-stage oftumor progression which means that it plays a role in tumor cellinvasion and metastasis. In earlier stages of tumor progression SPDEF issometimes up-regulated. De-regulation of SPDEF is described for severalcancer entities including breast, prostate and colorectal cancer (Moussaet al., 2009; Schaefer et al., 2010; Steffan and Koul, 2011). SPDEFinduces the transcription of E-cadherin and suppresses thereby cellinvasion and migration (Pal et al., 2013). SPDEF interacts withbeta-catenin and blocks the transcriptional activity resulting in lowerprotein levels of the oncogenes cyclin D1 and c-Myc (Noah et al., 2013).

SPON1 encodes spondin 1 and is located on chromosome 11p15.2 (RefSeq,2002). SPON1 is involved in cancer cell proliferation, migration,invasion, and metastasis. SPON1 is involved in Fak and Src signaling.SPON1 is involved in IL-6 maintenance via MEKK/p38 MAPK/NF-kappaBsignaling and this may support murine neuroblastoma survival (Chang etal., 2015a; Cheng et al., 2009; Dai et al., 2015). SPON1 isdown-regulated by miR-506 (Dai et al., 2015). SPON1 is over-expressed inovarian cancer (Davidson et al., 2011; Jiao et al., 2013; Pyle-Chenaultet al., 2005). SPON1 may have diagnostic potential in cancer prognosis(Pagnotta et al., 2013).

STAG3 encodes stromal antigen 3, which is expressed in the nucleus andis a subunit of the cohesin complex which regulates the cohesion ofsister chromatids during cell division (RefSeq, 2002). Researchers havereported the involvement of a common allele of STAG3 in the developmentof epithelial ovarian cancer. Another group has identified STAG3 to becapable of effectively discriminating lung cancer, chronic obstructivelung disease and fibrotic interstitial lung diseases. Others havedetected expression of the STAG3 gene in p53 mutated lymphoma cells(Notaridou et al., 2011; Wielscher et al., 2015; Kalejs et al., 2006).

TDRD5 encodes tudor domain containing 5 and is located on chromosome1q25.2 (RefSeq, 2002). TDRD5 may be over-expressed in breast cancer(Jiang et al., 2016). TDRD5 methylation is altered upon resveratroltreatment in triple negative breast cancer (Medina-Aguilar et al.,2017). TDRD5 is part of a run of homozygosity associated with thyroidcancer (Thomsen et al., 2016).

TENM4 encodes teneurin transmembrane protein 4 which is expressed in thenervous systems and mesenchymal tissues and is a regulator ofchondrogenesis (Suzuki et al., 2014). Among the four most frequentlymutated genes was TENM4 showing protein-changing mutations in primaryCNS lymphomas (Vater et al., 2015). MDA-MB-175 cell line contains achromosomal translocation that leads to the fusion of TENM4 andreceptors of the ErbB family. Chimeric genes were also found inneuroblastomas (Wang et al., 1999; Boeva et al., 2013).

TMPRSS3 encodes transmembrane protease, serine 3 which is a protein thatbelongs to the serine protease family. The encoded protein contains aserine protease domain, a transmembrane domain, an LDL receptor-likedomain, and a scavenger receptor cysteine-rich domain. Serine proteasesare known to be involved in a variety of biological processes, whosemalfunction often leads to human diseases and disorders. This gene wasidentified by its association with both congenital and childhood onsetautosomal recessive deafness. This gene is expressed in fetal cochleaand many other tissues, and is thought to be involved in the developmentand maintenance of the inner ear or the contents of the perilymph andendolymph. This gene was also identified as a tumor-associated gene thatis overexpressed in ovarian tumors (RefSeq, 2002). TMPRSS3 is involvedin cell proliferation, invasion, and migration. TMPRSS3 induces ERK1/2signaling (Zhang et al., 2016a). TMPRSS3 affects E-cadherin, vimentin,and Twist expression. TMPRSS3 is down-regulated by hexamethylenebisacetamide (Zhang et al., 2016a; Zhang et al., 2004). TMPRSS3 isup-regulated in breast cancer, pancreatic cancer, and ovarian cancer.TMPRSS3 is de-regulated in gastric cancer and pancreatic ductaladenocarcinoma (Rui et al., 2015; Zhang et al., 2016a; Zhang et al.,2004; Amsterdam et al., 2014; lacobuzio-Donahue et al., 2003; Luo etal., 2017; Underwood et al., 2000; Wallrapp et al., 2000). TMPRSS3 isassociated with TNM stage, lymph node metastasis, distant organmetastasis, shorter survival, shorter disease-free survival, and poorprognosis. TMPRSS3 may be used as biomarker in cancer. TMPRSS3 mutationsare associated with cancer risk. TMPRSS3 may be used for earlypancreatic ductal adenocarcinoma detection (Rui et al., 2015; Amsterdamet al., 2014; Luo et al., 2017; Dorn et al., 2014; Luostari et al.,2014; Pelkonen et al., 2015; Sawasaki et al., 2004). TMPRSS3 ishypo-methylated in cancer (Guerrero et al., 2012).

VTCN1, also known as B7-H4, encodes a member of the B7 costimulatoryprotein family which is present on the surface of antigen-presentingcells and interacts with ligands bound to receptors on the surface of Tcells (RefSeq, 2002). VTCN1 was shown to be up-regulated in lung cancer,colorectal cancer, hepatocellular carcinoma, osteosarcoma, breastcancer, cervical cancer, urothelial cell carcinoma, gastric cancer,endometrial cancer, thyroid cancer and laryngeal carcinoma (Klatka etal., 2013; Zhu et al., 2013; Vanderstraeten et al., 2014; Shi et al.,2014; Fan et al., 2014; Wang et al., 2014; Leong et al., 2015; Dong andMa, 2015; Zhang et al., 2015a; Peng et al., 2015; Xu et al., 2015a).VTCN1 is associated with poor overall survival and higher recurrenceprobability in hepatocellular carcinoma and poor overall survival inosteosarcoma, urothelial cell carcinoma, pancreatic cancer, gastriccancer, cervical cancer, melanoma and thyroid cancer (Zhu et al., 2013;Seliger, 2014; Liu et al., 2014b; Chen et al., 2014; Fan et al., 2014;Dong and Ma, 2015; Zhang et al., 2015a). VTCN1 is associated with clearcell renal cell carcinoma (Xu et al., 2014b). VTCN1 expression levelswere shown to be inversely correlated with patient survival in ovariancancer (Smith et al., 2014). VTCN1 may be a potential prognosticindicator of urothelial cell carcinoma and gastric cancer (Shi et al.,2014; Fan et al., 2014).

WNT7A encodes Wnt family member 7A which is a member of the WNT genefamily. These proteins have been implicated in oncogenesis and inseveral developmental processes, including regulation of cell fate andpatterning during embryogenesis. This gene is involved in thedevelopment of the anterior-posterior axis in the female reproductivetract, and also plays a critical role in uterine smooth muscle patteringand maintenance of adult uterine function. Mutations in this gene areassociated with Fuhrmann and Al-Awadi/Raas-Rothschild/Schinzelphocomelia syndromes (RefSeq, 2002). WNT7A is induced by STAT4 resultingin the activation of cancer-associated fibroblasts. WNT7A potentiatesTGF-beta receptor signaling. WNT7A is involved in cell proliferation andmigration. WNT7A is an upstream inducer of senescence. PG545 interactswith WNT7A resulting in inhibited cell proliferation. WNT7A suppressestumor growth. WNT7A is involved in Wnt/beta-catenin signaling andregulates hsa-miR29b (Avasarala et al., 2013; Avgustinova et al., 2016;Bikkavilli et al., 2015; Borowicz et al., 2014; Jung et al., 2015; Kinget al., 2015; Ramos-Solano et al., 2015; Zhao et al., 2017). WNT7A isregulated by miR-15b and down-regulated by DNMT1. Endosulfan disruptsWNT7A. WNT7A is a target gene of miR-199a-5p and miR-195/497. WNT7A isdown-regulated by chronic ethanol exposure and rescued by PPAR-deltaagonist treatment. Dkk-1 affects WNT7A. Bilobalide enhances WNT7Aexpression (Kim et al., 2015a; Chandra et al., 2014; Ingaramo et al.,2016; Itesako et al., 2014; Liu et al., 2014a; MacLean et al., 2016;Mercer et al., 2014; Mercer et al., 2015; Xu et al., 2015b). WNT7A isdown-regulated and hyper-methylated in cervical cancer. WNT7A is lost inlung cancer. WNT7A is over-expressed in endometrial cancer (Ramos-Solanoet al., 2015; Kim et al., 2015b; Liu et al., 2013). WNT7A expressioncorrelates with poor prognosis and poor patient outcome. WNT7A promotormethylation correlates with advanced tumor stage, distant metastasis,and loss of E-cadherin. Decreased WNT7A expression correlates withdecreased overall survival in malignant pleural mesothelioma and may beused for chemosensitivity prediction (Avgustinova et al., 2016; King etal., 2015; Kim et al., 2015b; Hirata et al., 2015). WNT7A may be a tumorsuppressor gene in nasopharyngeal cancer (Nawaz et al., 2015).

DETAILED DESCRIPTION OF THE INVENTION

Stimulation of an immune response is dependent upon the presence ofantigens recognized as foreign by the host immune system. The discoveryof the existence of tumor associated antigens has raised the possibilityof using a host's immune system to intervene in tumor growth. Variousmechanisms of harnessing both the humoral and cellular arms of theimmune system are currently being explored for cancer immunotherapy.

Specific elements of the cellular immune response are capable ofspecifically recognizing and destroying tumor cells. The isolation ofT-cells from tumor-infiltrating cell populations or from peripheralblood suggests that such cells play an important role in natural immunedefense against cancer. CD8-positive T-cells in particular, whichrecognize class I molecules of the major histocompatibility complex(MHC)-bearing peptides of usually 8 to 10 amino acid residues derivedfrom proteins or defect ribosomal products (DRIPS) located in thecytosol, play an important role in this response. The MHC-molecules ofthe human are also designated as human leukocyte-antigens (HLA).

The term “T-cell response” means the specific proliferation andactivation of effector functions induced by a peptide in vitro or invivo. For MHC class I restricted cytotoxic T cells, effector functionsmay be lysis of peptide-pulsed, peptide-precursor pulsed or naturallypeptide-presenting target cells, secretion of cytokines, preferablyInterferon-gamma, TNF-alpha, or IL-2 induced by peptide, secretion ofeffector molecules, preferably granzymes or perforins induced bypeptide, or degranulation.

The term “peptide” is used herein to designate a series of amino acidresidues, connected one to the other typically by peptide bonds betweenthe alpha-amino and carbonyl groups of the adjacent amino acids. Thepeptides are preferably 9 amino acids in length, but can be as short as8 amino acids in length, and as long as 10, 11, or 12 or longer, and incase of MHC class II peptides (elongated variants of the peptides of theinvention) they can be as long as 13, 14, 15, 16, 17, 18, 19 or 20 ormore amino acids in length.

Furthermore, the term “peptide” shall include salts of a series of aminoacid residues, connected one to the other typically by peptide bondsbetween the alpha-amino and carbonyl groups of the adjacent amino acids.Preferably, the salts are pharmaceutical acceptable salts of thepeptides, such as, for example, the chloride or acetate(trifluoroacetate) salts. It has to be noted that the salts of thepeptides according to the present invention differ substantially fromthe peptides in their state(s) in vivo, as the peptides are not salts invivo.

The term “peptide” shall also include “oligopeptide”. The term“oligopeptide” is used herein to designate a series of amino acidresidues, connected one to the other typically by peptide bonds betweenthe alpha-amino and carbonyl groups of the adjacent amino acids. Thelength of the oligopeptide is not critical to the invention, as long asthe correct epitope or epitopes are maintained therein. Theoligopeptides are typically less than about 30 amino acid residues inlength, and greater than about 15 amino acids in length.

The term “polypeptide” designates a series of amino acid residues,connected one to the other typically by peptide bonds between thealpha-amino and carbonyl groups of the adjacent amino acids. The lengthof the polypeptide is not critical to the invention as long as thecorrect epitopes are maintained. In contrast to the terms peptide oroligopeptide, the term polypeptide is meant to refer to moleculescontaining more than about 30 amino acid residues.

A peptide, oligopeptide, protein or polynucleotide coding for such amolecule is “immunogenic” (and thus is an “immunogen” within the presentinvention), if it is capable of inducing an immune response. In the caseof the present invention, immunogenicity is more specifically defined asthe ability to induce a T-cell response. Thus, an “immunogen” would be amolecule that is capable of inducing an immune response, and in the caseof the present invention, a molecule capable of inducing a T-cellresponse. In another aspect, the immunogen can be the peptide, thecomplex of the peptide with MHC, oligopeptide, and/or protein that isused to raise specific antibodies or TCRs against it.

A class I T cell “epitope” requires a short peptide that is bound to aclass I MHC receptor, forming a ternary complex (MHC class I alphachain, beta-2-microglobulin, and peptide) that can be recognized by a Tcell bearing a matching T-cell receptor binding to the MHC/peptidecomplex with appropriate affinity. Peptides binding to MHC class Imolecules are typically 8-14 amino acids in length, and most typically 9amino acids in length.

In humans, there are three different genetic loci that encode MHC classI molecules (the MHC-molecules of the human are also designated humanleukocyte antigens (HLA)): HLA-A, HLA-B, and HLA-C. HLA-A*01, HLA-A*02,and HLA-B*07 are examples of different MHC class I alleles that can beexpressed from these loci.

TABLE 6 Expression frequencies F of HLA-A*02, HLA-A*01, HLA-A*03,HLA-A*24, HLA-B*07, HLA-B*08 and HLA-B*44 serotypes. Haplotypefrequencies Gf are derived from a study which used HLA-typing data froma registry of more than 6.5 million volunteer donors in the U.S.(Gragert et al., 2013). The haplotype frequency is the frequency of adistinct allele on an individual chromosome. Due to the diploid set ofchromosomes within mammalian cells, the frequency of genotypicoccurrence of this allele is higher and can be calculated employing theHardy-Weinberg principle (F = 1 − (1 − Gf)²). Calculated phenotype fromAllele Population allele frequency (F) A*02 African (N = 28557) 32.3%European Caucasian 49.3% (N = 1242890) Japanese (N = 24582) 42.7%Hispanic, S + Cent Amer. 46.1% (N = 146714) Southeast Asian (N = 27978)30.4% A*01 African (N = 28557) 10.2% European Caucasian 30.2% (N =1242890) Japanese (N = 24582) 1.8% Hispanic, S + Cent Amer. 14.0% (N =146714) Southeast Asian (N = 27978) 21.0% A*03 African (N = 28557) 14.8%European Caucasian 26.4% (N = 1242890) Japanese (N = 24582) 1.8%Hispanic, S + Cent Amer. 14.4% (N = 146714) Southeast Asian (N = 27978)10.6% A*24 African (N = 28557) 2.0% European Caucasian 8.6% (N =1242890) Japanese (N = 24582) 35.5% Hispanic, S + Cent Amer. 13.6% (N =146714) Southeast Asian (N = 27978) 16.9% B*07 African (N = 28557) 14.7%European Caucasian 25.0% (N = 1242890) Japanese (N = 24582) 11.4%Hispanic, S + Cent Amer. 12.2% (N = 146714) Southeast Asian (N = 27978)10.4% B*08 African (N = 28557) 6.0% European Caucasian 21.6% (N =1242890) Japanese (N = 24582) 1.0% Hispanic, S + Cent Amer. 7.6% (N =146714) Southeast Asian (N = 27978) 6.2% B*44 African (N = 28557) 10.6%European Caucasian 26.9% (N = 1242890) Japanese (N = 24582) 13.0%Hispanic, S + Cent Amer. 18.2% (N = 146714) Southeast Asian (N = 27978)13.1%

The peptides of the invention, preferably when included into a vaccineof the invention as described herein bind to A*02, A*01, A*03, A*24,B*07, B*08 or B*44. A vaccine may also include pan-binding MHC class IIpeptides. Therefore, the vaccine of the invention can be used to treatcancer in patients that are A*02-, A*01-, A*03-, A*24-, B*07-, B*08- orB*44-positive, whereas no selection for MHC class II allotypes isnecessary due to the pan-binding nature of these peptides.

If A*02 peptides of the invention are combined with peptides binding toanother allele, for example A*24, a higher percentage of any patientpopulation can be treated compared with addressing either MHC class Iallele alone. While in most populations less than 50% of patients couldbe addressed by either allele alone, a vaccine comprising HLA-A*24 andHLA-A*02 epitopes can treat at least 60% of patients in any relevantpopulation. Specifically, the following percentages of patients will bepositive for at least one of these alleles in various regions: USA 61%,Western Europe 62%, China 75%, South Korea 77%, Japan 86%.

TABLE 7 HLA alleles coverage in European Caucasian population(calculated from (Gragert et al., 2013)). coverage (at least combinedone A- combined combined with B*07 allele) with B*07 with B*44 and B*44A*02/A*01 70% 78% 78% 84% A*02/A*03 68% 76% 76% 83% A*02/A*24 61% 71%71% 80% A*′01/A*03 52% 64% 65% 75% A*01/A*24 44% 58% 59% 71% A*03/A*2440% 55% 56% 69% A*02/A*01/A*03 84% 88% 88% 91% A*02/A*01/A*24 79% 84%84% 89% A*02/A*03/A*24 77% 82% 83% 88% A*01/A*03/A*24 63% 72% 73% 81%A*02/A*01/A*03/A*24 90% 92% 93% 95%

In a preferred embodiment, the term “nucleotide sequence” refers to aheteropolymer of deoxyribonucleotides.

The nucleotide sequence coding for a particular peptide, oligopeptide,or polypeptide may be naturally occurring or they may be syntheticallyconstructed. Generally, DNA segments encoding the peptides,polypeptides, and proteins of this invention are assembled from cDNAfragments and short oligonucleotide linkers, or from a series ofoligonucleotides, to provide a synthetic gene that is capable of beingexpressed in a recombinant transcriptional unit comprising regulatoryelements derived from a microbial or viral operon.

As used herein the term “a nucleotide coding for (or encoding) apeptide” refers to a nucleotide sequence coding for the peptideincluding artificial (man-made) start and stop codons compatible for thebiological system the sequence is to be expressed by, for example, adendritic cell or another cell system useful for the production of TCRs.

As used herein, reference to a nucleic acid sequence includes bothsingle stranded and double stranded nucleic acid. Thus, for example forDNA, the specific sequence, unless the context indicates otherwise,refers to the single strand DNA of such sequence, the duplex of suchsequence with its complement (double stranded DNA) and the complement ofsuch sequence.

The term “coding region” refers to that portion of a gene which eithernaturally or normally codes for the expression product of that gene inits natural genomic environment, i.e., the region coding in vivo for thenative expression product of the gene.

The coding region can be derived from a non-mutated (“normal”), mutatedor altered gene, or can even be derived from a DNA sequence, or gene,wholly synthesized in the laboratory using methods well known to thoseof skill in the art of DNA synthesis.

The term “expression product” means the polypeptide or protein that isthe natural translation product of the gene and any nucleic acidsequence coding equivalents resulting from genetic code degeneracy andthus coding for the same amino acid(s).

The term “fragment”, when referring to a coding sequence, means aportion of DNA comprising less than the complete coding region, whoseexpression product retains essentially the same biological function oractivity as the expression product of the complete coding region.

The term “DNA segment” refers to a DNA polymer, in the form of aseparate fragment or as a component of a larger DNA construct, which hasbeen derived from DNA isolated at least once in substantially pure form,i.e., free of contaminating endogenous materials and in a quantity orconcentration enabling identification, manipulation, and recovery of thesegment and its component nucleotide sequences by standard biochemicalmethods, for example, by using a cloning vector. Such segments areprovided in the form of an open reading frame uninterrupted by internalnon-translated sequences, or introns, which are typically present ineukaryotic genes. Sequences of non-translated DNA may be presentdownstream from the open reading frame, where the same do not interferewith manipulation or expression of the coding regions.

The term “primer” means a short nucleic acid sequence that can be pairedwith one strand of DNA and provides a free 3′-OH end at which a DNApolymerase starts synthesis of a deoxyribonucleotide chain.

The term “promoter” means a region of DNA involved in binding of RNApolymerase to initiate transcription.

The term “isolated” means that the material is removed from its originalenvironment (e.g., the natural environment, if it is naturallyoccurring). For example, a naturally-occurring polynucleotide orpolypeptide present in a living animal is not isolated, but the samepolynucleotide or polypeptide, separated from some or all of thecoexisting materials in the natural system, is isolated. Suchpolynucleotides could be part of a vector and/or such polynucleotides orpolypeptides could be part of a composition, and still be isolated inthat such vector or composition is not part of its natural environment.

The polynucleotides, and recombinant or immunogenic polypeptides,disclosed in accordance with the present invention may also be in“purified” form. The term “purified” does not require absolute purity;rather, it is intended as a relative definition, and can includepreparations that are highly purified or preparations that are onlypartially purified, as those terms are understood by those of skill inthe relevant art. For example, individual clones isolated from a cDNAlibrary have been conventionally purified to electrophoretichomogeneity. Purification of starting material or natural material to atleast one order of magnitude, preferably two or three orders, and morepreferably four or five orders of magnitude is expressly contemplated.Furthermore, a claimed polypeptide which has a purity of preferably99.999%, or at least 99.99% or 99.9%; and even desirably 99% by weightor greater is expressly encompassed.

The nucleic acids and polypeptide expression products disclosedaccording to the present invention, as well as expression vectorscontaining such nucleic acids and/or such polypeptides, may be in“enriched form”. As used herein, the term “enriched” means that theconcentration of the material is at least about 2, 5, 10, 100, or 1000times its natural concentration (for example), advantageously 0.01%, byweight, preferably at least about 0.1% by weight. Enriched preparationsof about 0.5%, 1%, 5%, 10%, and 20% by weight are also contemplated. Thesequences, constructs, vectors, clones, and other materials comprisingthe present invention can advantageously be in enriched or isolatedform. The term “active fragment” means a fragment, usually of a peptide,polypeptide or nucleic acid sequence, that generates an immune response(i.e., has immunogenic activity) when administered, alone or optionallywith a suitable adjuvant or in a vector, to an animal, such as a mammal,for example, a rabbit or a mouse, and also including a human, suchimmune response taking the form of stimulating a T-cell response withinthe recipient animal, such as a human. Alternatively, the “activefragment” may also be used to induce a T-cell response in vitro.

As used herein, the terms “portion”, “segment” and “fragment”, when usedin relation to polypeptides, refer to a continuous sequence of residues,such as amino acid residues, which sequence forms a subset of a largersequence. For example, if a polypeptide were subjected to treatment withany of the common endopeptidases, such as trypsin or chymotrypsin, theoligopeptides resulting from such treatment would represent portions,segments or fragments of the starting polypeptide. When used in relationto polynucleotides, these terms refer to the products produced bytreatment of said polynucleotides with any of the endonucleases.

In accordance with the present invention, the term “percent identity” or“percent identical”, when referring to a sequence, means that a sequenceis compared to a claimed or described sequence after alignment of thesequence to be compared (the “Compared Sequence”) with the described orclaimed sequence (the “Reference Sequence”). The percent identity isthen determined according to the following formula:percent identity=100[1−(C/R)]wherein C is the number of differences between the Reference Sequenceand the Compared Sequence over the length of alignment between theReference Sequence and the Compared Sequence, wherein(i) each base or amino acid in the Reference Sequence that does not havea corresponding aligned base or amino acid in the Compared Sequence and(ii) each gap in the Reference Sequence and(iii) each aligned base or amino acid in the Reference Sequence that isdifferent from an aligned base or amino acid in the Compared Sequence,constitutes a difference and(iiii) the alignment has to start at position 1 of the alignedsequences;and R is the number of bases or amino acids in the Reference Sequenceover the length of the alignment with the Compared Sequence with any gapcreated in the Reference Sequence also being counted as a base or aminoacid.

If an alignment exists between the Compared Sequence and the ReferenceSequence for which the percent identity as calculated above is aboutequal to or greater than a specified minimum Percent Identity then theCompared Sequence has the specified minimum percent identity to theReference Sequence even though alignments may exist in which the hereinabove calculated percent identity is less than the specified percentidentity.

As mentioned above, the present invention thus provides a peptidecomprising a sequence that is selected from the group of consisting ofSEQ ID NO: 1 to SEQ ID NO: 772 or a variant thereof which is 88%homologous to SEQ ID NO: 1 to SEQ ID NO: 772, or a variant thereof thatwill induce T cells cross-reacting with said peptide. The peptides ofthe invention have the ability to bind to a molecule of the human majorhistocompatibility complex (MHC) class-I or elongated versions of saidpeptides to class II.

In the present invention, the term “homologous” refers to the degree ofidentity (see percent identity above) between sequences of two aminoacid sequences, i.e. peptide or polypeptide sequences. Theaforementioned “homology” is determined by comparing two sequencesaligned under optimal conditions over the sequences to be compared. Sucha sequence homology can be calculated by creating an alignment using,for example, the ClustalW algorithm. Commonly available sequenceanalysis software, more specifically, Vector NTI, GENETYX or other toolsare provided by public databases.

A person skilled in the art will be able to assess, whether T cellsinduced by a variant of a specific peptide will be able to cross-reactwith the peptide itself (Appay et al., 2006; Colombetti et al., 2006;Fong et al., 2001; Zaremba et al., 1997).

By a “variant” of the given amino acid sequence the inventors mean thatthe side chains of, for example, one or two of the amino acid residuesare altered (for example by replacing them with the side chain ofanother naturally occurring amino acid residue or some other side chain)such that the peptide is still able to bind to an HLA molecule insubstantially the same way as a peptide consisting of the given aminoacid sequence in consisting of SEQ ID NO: 1 to SEQ ID NO: 772. Forexample, a peptide may be modified so that it at least maintains, if notimproves, the ability to interact with and bind to the binding groove ofa suitable MHC molecule, such as HLA-A*02 or -DR, and in that way it atleast maintains, if not improves, the ability to bind to the TCR ofactivated T cells.

These T cells can subsequently cross-react with cells and kill cellsthat express a polypeptide that contains the natural amino acid sequenceof the cognate peptide as defined in the aspects of the invention. Ascan be derived from the scientific literature and databases (Rammenseeet al., 1999; Godkin et al., 1997), certain positions of HLA bindingpeptides are typically anchor residues forming a core sequence fittingto the binding motif of the HLA receptor, which is defined by polar,electrophysical, hydrophobic and spatial properties of the polypeptidechains constituting the binding groove. Thus, one skilled in the artwould be able to modify the amino acid sequences set forth in SEQ ID NO:1 to SEQ ID NO 772, by maintaining the known anchor residues, and wouldbe able to determine whether such variants maintain the ability to bindMHC class I or II molecules. The variants of the present inventionretain the ability to bind to the TCR of activated T cells, which cansubsequently cross-react with and kill cells that express a polypeptidecontaining the natural amino acid sequence of the cognate peptide asdefined in the aspects of the invention.

The original (unmodified) peptides as disclosed herein can be modifiedby the substitution of one or more residues at different, possiblyselective, sites within the peptide chain, if not otherwise stated.Preferably those substitutions are located at the end of the amino acidchain. Such substitutions may be of a conservative nature, for example,where one amino acid is replaced by an amino acid of similar structureand characteristics, such as where a hydrophobic amino acid is replacedby another hydrophobic amino acid. Even more conservative would bereplacement of amino acids of the same or similar size and chemicalnature, such as where leucine is replaced by isoleucine. In studies ofsequence variations in families of naturally occurring homologousproteins, certain amino acid substitutions are more often tolerated thanothers, and these are often show correlation with similarities in size,charge, polarity, and hydrophobicity between the original amino acid andits replacement, and such is the basis for defining “conservativesubstitutions.”

Conservative substitutions are herein defined as exchanges within one ofthe following five groups: Group 1-small aliphatic, nonpolar or slightlypolar residues (Ala, Ser, Thr, Pro, Gly); Group 2-polar, negativelycharged residues and their amides (Asp, Asn, Glu, Gln); Group 3-polar,positively charged residues (His, Arg, Lys); Group 4-large, aliphatic,nonpolar residues (Met, Leu, Ile, Val, Cys); and Group 5-large, aromaticresidues (Phe, Tyr, Trp).

Less conservative substitutions might involve the replacement of oneamino acid by another that has similar characteristics but is somewhatdifferent in size, such as replacement of an alanine by an isoleucineresidue. Highly non-conservative replacements might involve substitutingan acidic amino acid for one that is polar, or even for one that isbasic in character. Such “radical” substitutions cannot, however, bedismissed as potentially ineffective since chemical effects are nottotally predictable and radical substitutions might well give rise toserendipitous effects not otherwise predictable from simple chemicalprinciples.

Of course, such substitutions may involve structures other than thecommon L-amino acids. Thus, D-amino acids might be substituted for theL-amino acids commonly found in the antigenic peptides of the inventionand yet still be encompassed by the disclosure herein. In addition,non-standard amino acids (i.e., other than the common naturallyoccurring proteinogenic amino acids) may also be used for substitutionpurposes to produce immunogens and immunogenic polypeptides according tothe present invention.

If substitutions at more than one position are found to result in apeptide with substantially equivalent or greater antigenic activity asdefined below, then combinations of those substitutions will be testedto determine if the combined substitutions result in additive orsynergistic effects on the antigenicity of the peptide. At most, no morethan 4 positions within the peptide would be simultaneously substituted.

A peptide consisting essentially of the amino acid sequence as indicatedherein can have one or two non-anchor amino acids (see below regardingthe anchor motif) exchanged without that the ability to bind to amolecule of the human major histocompatibility complex (MHC) class-I or—II is substantially changed or is negatively affected, when compared tothe non-modified peptide. In another embodiment, in a peptide consistingessentially of the amino acid sequence as indicated herein, one or twoamino acids can be exchanged with their conservative exchange partners(see herein below) without that the ability to bind to a molecule of thehuman major histocompatibility complex (MHC) class-I or —II issubstantially changed, or is negatively affected, when compared to thenon-modified peptide.

The amino acid residues that do not substantially contribute tointeractions with the T-cell receptor can be modified by replacementwith other amino acid whose incorporation does not substantially affectT-cell reactivity and does not eliminate binding to the relevant MHC.Thus, apart from the proviso given, the peptide of the invention may beany peptide (by which term the inventors include oligopeptide orpolypeptide), which includes the amino acid sequences or a portion orvariant thereof as given.

TABLE 8  Variants and motif of the peptides accordingto SEQ ID NO: 3, 225, 13, 17, 84, 108, 113, 114, 147, 36, 51, 172, 54, and 57 Position 1 2 3 4 5 6 7 8 9SEQ ID No 3 A L I Y N L V G I Variant V L A M V M M L M A A V A A L A AV V V V L V A T V T T L T A Q V Q Q L Q A Position 1 2 3 4 5 6 7 8 9SEQ ID No 225 S V F A H P R K L Variant L V L I L L A M V M I M M A A VA I A A A V I A T V T I T T A Q V Q I Q Q A Position 1 2 3 4 5 6 7 8 9SEQ ID No 13 V Y T F L S S T L Variant I F F I F F F Position 1 2 3 4 56 7 8 9 SEQ ID No 17 R F T T M L S T F Variant Y I Y L Y I L Position 12 3 4 5 6 7 8 9 10 SEQ ID No 84 K L Q P A Q T A A K Variant Y R F I I YI R I F M M Y M R M F V V Y V R V F T T Y T R T F Position 1 2 3 4 5 6 78 9 10 SEQ ID No 108 V L Y P V P L E S Y Variant K R F I K I I R I F M KM M R M F V K V V R V F T K T T R T F Position 1 2 3 4 5 6 7 8 9SEQ ID No 113 Q L D S N R L T Y Variant S S A S E S E A T T A T E T E APosition 1 2 3 4 5 6 7 8 9 10 SEQ ID No 114 V M E Q S A G I M Y VariantS D S D A S S A T D T D A T T A Position 1 2 3 4 5 6 7 8 9 10 11SEQ ID No 147 A P R W F P Q P T V V Variant L F M A I Position 1 2 3 4 56 7 8 9 SEQ ID No 36 A P A A W L R S A Variant L F V M I Position 1 2 34 5 6 7 8 9 SEQ ID No 51 S L R L K N V Q L Variant K K V K I K M K F K RK R V K R I K R M K R F K H K H V K H I K H M K H F V I M F R R V R I RM R F H H V H I H M H F L L V L I L M L F L R L R V L R I L R M L R F LH L H V L H I L H M L H F Position 1 2 3 4 5 6 7 8 9 SEQ ID No 172 K L KE R N R E L Variant K K V K I K M K F V I M F H H V H I H M H F R K R KV R K I R K M R K F R R V R I R M R F R H R H V R H I R H M R H F L K LK V L K I L K M L K F L L V L I L M L F L H L H V L H I L H M L H FPosition 1 2 3 4 5 6 7 8 9 10 11 SEQ ID No 54 A E I T I T T Q T G YVariant F W L D F D W D L D Position 1 2 3 4 5 6 7 8 9 SEQ ID No 57 Q ES D L R L F L Variant F W Y D F D W D Y D

Longer (elongated) peptides may also be suitable. It is possible thatMHC class I epitopes, although usually between 8 and 11 amino acidslong, are generated by peptide processing from longer peptides orproteins that include the actual epitope. It is preferred that theresidues that flank the actual epitope are residues that do notsubstantially affect proteolytic cleavage necessary to expose the actualepitope during processing.

The peptides of the invention can be elongated by up to four aminoacids, that is 1, 2, 3 or 4 amino acids can be added to either end inany combination between 4:0 and 0:4. Combinations of the elongationsaccording to the invention can be found in Table 9.

TABLE 9 Combinations of the elongations of peptides of the inventionC-terminus N-terminus 4 0 3 0 or 1 2 0 or 1 or 2 1 0 or 1 or 2 or 3 0 0or 1 or 2 or 3 or 4 N-terminus C-terminus 4 0 3 0 or 1 2 0 or 1 or 2 1 0or 1 or 2 or 3 0 0 or 1 or 2 or 3 or 4

The amino acids for the elongation/extension can be the peptides of theoriginal sequence of the protein or any other amino acid(s). Theelongation can be used to enhance the stability or solubility of thepeptides.

Thus, the epitopes of the present invention may be identical tonaturally occurring tumor-associated or tumor-specific epitopes or mayinclude epitopes that differ by no more than four residues from thereference peptide, as long as they have substantially identicalantigenic activity.

In an alternative embodiment, the peptide is elongated on either or bothsides by more than 4 amino acids, preferably to a total length of up to30 amino acids. This may lead to MHC class II binding peptides. Bindingto MHC class II can be tested by methods known in the art.

Accordingly, the present invention provides peptides and variants of MHCclass I epitopes, wherein the peptide or variant has an overall lengthof between 8 and 100, preferably between 8 and 30, and most preferredbetween 8 and 14, namely 8, 9, 10, 11, 12, 13, 14 amino acids, in caseof the elongated class II binding peptides the length can also be 15,16, 17, 18, 19, 20, 21, 22, 23, 24 or 25 amino acids.

Of course, the peptide or variant according to the present inventionwill have the ability to bind to a molecule of the human majorhistocompatibility complex (MHC) class I or II. Binding of a peptide ora variant to a MHC complex may be tested by methods known in the art.

Preferably, when the T cells specific for a peptide according to thepresent invention are tested against the substituted peptides, thepeptide concentration at which the substituted peptides achieve half themaximal increase in lysis relative to background is no more than about 1mM, preferably no more than about 1 μM, more preferably no more thanabout 1 nM, and still more preferably no more than about 100 pM, andmost preferably no more than about 10 pM. It is also preferred that thesubstituted peptide be recognized by T cells from more than oneindividual, at least two, and more preferably three individuals.

In a particularly preferred embodiment of the invention the peptideconsists or consists essentially of an amino acid sequence according toSEQ ID NO: 1 to SEQ ID NO: 772.

“Consisting essentially of” shall mean that a peptide according to thepresent invention, in addition to the sequence according to any of SEQID NO: 1 to SEQ ID NO 772 or a variant thereof contains additional N-and/or C-terminally located stretches of amino acids that are notnecessarily forming part of the peptide that functions as an epitope forMHC molecules epitope.

Nevertheless, these stretches can be important to provide an efficientintroduction of the peptide according to the present invention into thecells. In one embodiment of the present invention, the peptide is partof a fusion protein which comprises, for example, the 80 N-terminalamino acids of the HLA-DR antigen-associated invariant chain (p33, inthe following “Ii”) as derived from the NCBI, GenBank Accession numberX00497. In other fusions, the peptides of the present invention can befused to an antibody as described herein, or a functional part thereof,in particular into a sequence of an antibody, so as to be specificallytargeted by said antibody, or, for example, to or into an antibody thatis specific for dendritic cells as described herein.

In addition, the peptide or variant may be modified further to improvestability and/or binding to MHC molecules in order to elicit a strongerimmune response. Methods for such an optimization of a peptide sequenceare well known in the art and include, for example, the introduction ofreverse peptide bonds or non-peptide bonds.

In a reverse peptide bond amino acid residues are not joined by peptide(—CO—NH—) linkages but the peptide bond is reversed. Such retro-inversopeptidomimetics may be made using methods known in the art, for examplesuch as those described in Meziere et al (1997) (Meziere et al., 1997),incorporated herein by reference. This approach involves makingpseudopeptides containing changes involving the backbone, and not theorientation of side chains. Meziere et al. (Meziere et al., 1997) showthat for MHC binding and T helper cell responses, these pseudopeptidesare useful. Retro-inverse peptides, which contain NH—CO bonds instead ofCO—NH peptide bonds, are much more resistant to proteolysis.

A non-peptide bond is, for example, —CH₂—NH, —CH₂S—, —CH₂CH₂—, —CH═CH—,—COCH₂—, —CH(OH)CH₂—, and —CH₂SO—. U.S. Pat. No. 4,897,445 provides amethod for the solid phase synthesis of non-peptide bonds (—CH₂—NH) inpolypeptide chains which involves polypeptides synthesized by standardprocedures and the non-peptide bond synthesized by reacting an aminoaldehyde and an amino acid in the presence of NaCNBH₃.

Peptides comprising the sequences described above may be synthesizedwith additional chemical groups present at their amino and/or carboxytermini, to enhance the stability, bioavailability, and/or affinity ofthe peptides. For example, hydrophobic groups such as carbobenzoxyl,dansyl, or t-butyloxycarbonyl groups may be added to the peptides' aminotermini. Likewise, an acetyl group or a 9-fluorenylmethoxy-carbonylgroup may be placed at the peptides' amino termini. Additionally, thehydrophobic group, t-butyloxycarbonyl, or an amido group may be added tothe peptides' carboxy termini.

Further, the peptides of the invention may be synthesized to alter theirsteric configuration. For example, the D-isomer of one or more of theamino acid residues of the peptide may be used, rather than the usualL-isomer. Still further, at least one of the amino acid residues of thepeptides of the invention may be substituted by one of the well-knownnon-naturally occurring amino acid residues. Alterations such as thesemay serve to increase the stability, bioavailability and/or bindingaction of the peptides of the invention.

Similarly, a peptide or variant of the invention may be modifiedchemically by reacting specific amino acids either before or aftersynthesis of the peptide. Examples for such modifications are well knownin the art and are summarized e.g. in R. Lundblad, Chemical Reagents forProtein Modification, 3rd ed. CRC Press, 2004 (Lundblad, 2004), which isincorporated herein by reference. Chemical modification of amino acidsincludes but is not limited to, modification by acylation, amidination,pyridoxylation of lysine, reductive alkylation, trinitrobenzylation ofamino groups with 2,4,6-trinitrobenzene sulphonic acid (TNBS), amidemodification of carboxyl groups and sulphydryl modification by performicacid oxidation of cysteine to cysteic acid, formation of mercurialderivatives, formation of mixed disulphides with other thiol compounds,reaction with maleimide, carboxymethylation with iodoacetic acid oriodoacetamide and carbamoylation with cyanate at alkaline pH, althoughwithout limitation thereto. In this regard, the skilled person isreferred to Chapter 15 of Current Protocols In Protein Science, Eds.Coligan et al. (John Wiley and Sons NY 1995-2000) (Coligan et al., 1995)for more extensive methodology relating to chemical modification ofproteins.

Briefly, modification of e.g. arginyl residues in proteins is oftenbased on the reaction of vicinal dicarbonyl compounds such asphenylglyoxal, 2,3-butanedione, and 1,2-cyclohexanedione to form anadduct. Another example is the reaction of methylglyoxal with arginineresidues. Cysteine can be modified without concomitant modification ofother nucleophilic sites such as lysine and histidine. As a result, alarge number of reagents are available for the modification of cysteine.The websites of companies such as Sigma-Aldrich provide information onspecific reagents.

Selective reduction of disulfide bonds in proteins is also common.Disulfide bonds can be formed and oxidized during the heat treatment ofbiopharmaceuticals. Woodward's Reagent K may be used to modify specificglutamic acid residues. N-(3-(dimethylamino)propyl)-N′-ethylcarbodiimidecan be used to form intra-molecular crosslinks between a lysine residueand a glutamic acid residue. For example, diethylpyrocarbonate is areagent for the modification of histidyl residues in proteins. Histidinecan also be modified using 4-hydroxy-2-nonenal. The reaction of lysineresidues and other α-amino groups is, for example, useful in binding ofpeptides to surfaces or the cross-linking of proteins/peptides. Lysineis the site of attachment of poly(ethylene)glycol and the major site ofmodification in the glycosylation of proteins. Methionine residues inproteins can be modified with e.g. iodoacetamide, bromoethylamine, andchloramine T.

Tetranitromethane and N-acetylimidazole can be used for the modificationof tyrosyl residues. Cross-linking via the formation of dityrosine canbe accomplished with hydrogen peroxide/copper ions.

Recent studies on the modification of tryptophan have usedN-bromosuccinimide, 2-hydroxy-5-nitrobenzyl bromide or3-bromo-3-methyl-2-(2-nitrophenylmercapto)-3H-indole (BPNS-skatole).

Successful modification of therapeutic proteins and peptides with PEG isoften associated with an extension of circulatory half-life whilecross-linking of proteins with glutaraldehyde, polyethylene glycoldiacrylate and formaldehyde is used for the preparation of hydrogels.Chemical modification of allergens for immunotherapy is often achievedby carbamylation with potassium cyanate.

A peptide or variant, wherein the peptide is modified or includesnon-peptide bonds is a preferred embodiment of the invention.

Another embodiment of the present invention relates to a non-naturallyoccurring peptide wherein said peptide consists or consists essentiallyof an amino acid sequence according to SEQ ID No: 1 to SEQ ID No: 772and has been synthetically produced (e.g. synthesized) as apharmaceutically acceptable salt. Methods to synthetically producepeptides are well known in the art. The salts of the peptides accordingto the present invention differ substantially from the peptides in theirstate(s) in vivo, as the peptides as generated in vivo are no salts. Thenon-natural salt form of the peptide mediates the solubility of thepeptide, in particular in the context of pharmaceutical compositionscomprising the peptides, e.g. the peptide vaccines as disclosed herein.A sufficient and at least substantial solubility of the peptide(s) isrequired in order to efficiently provide the peptides to the subject tobe treated. Preferably, the salts are pharmaceutically acceptable saltsof the peptides. These salts according to the invention include alkalineand earth alkaline salts such as salts of the Hofmeister seriescomprising as anions PO₄ ³⁻, SO₄ ²⁻, CH₃COO⁻, Cl⁻, Br⁻, NO₃ ⁻, ClO₄ ⁻,I⁻, SCN⁻ and as cations NH₄ ⁺, Rb⁺, K⁺, Na⁺, Cs⁺, Li⁺, Zn²⁺, Mg²⁺, Ca²⁺,Mn²⁺, Cu²⁺ and Ba²⁺. Particularly salts are selected from (NH₄)₃PO₄,(NH₄)₂HPO₄, (NH₄)H₂PO₄, (NH₄)₂SO₄, NH₄CH₃COO, NH₄Ck, NH₄Br, NH₄NO₃,NH₄ClO₄, NH₄I, NH₄SCN, Rb₃PO₄, Rb₂HPO₄, RbH₂PO₄, Rb₂SO₄, Rb₄CH₃COO,Rb₄Cl, Rb₄Br, Rb₄NO₃, Rb₄ClO₄, Rb₄I, Rb₄SCN, K₃PO₄, K₂HPO₄, KH₂PO₄,K₂SO₄, KCH₃COO, KCl, KBr, KNOB, KClO₄, KI, KSCN, Na₃PO₄, Na₂HPO₄,NaH₂PO₄, Na₂SO₄, NaCH₃COO, NaCl, NaBr, NaNO₃, NaClO₄, NaI, NaSCN, ZnCl₂Cs₃PO₄, Cs₂HPO₄, CsH₂PO₄, Cs₂SO₄, CsCH₃COO, CsCl, CsBr, CsNO₃, CsClO₄,CsI, CsSCN, Li₃PO₄, Li₂HPO₄, LiH₂PO₄, Li₂SO₄, LiCH₃COO, LiCl, LiBr,LiNO₃, LiClO₄, LiI, LiSCN, Cu₂SO₄, Mg₃(PO₄)₂, Mg₂HPO₄, Mg(H₂PO₄)₂,Mg₂SO₄, Mg(CH₃COO)₂, MgCl₂, MgBr₂, Mg(NO₃)₂, Mg(ClO₄)₂, MgI₂, Mg(SCN)₂,MnCl₂, Ca₃(PO₄), Ca₂HPO₄, Ca(H₂PO₄)₂, CaSO₄, Ca(CH₃COO)₂, CaCl₂), CaBr₂,Ca(NO₃)₂, Ca(ClO₄)₂, CaI₂, Ca(SCN)₂, Ba₃(PO₄)₂, Ba₂HPO₄, Ba(H₂PO₄)₂,BaSO₄, Ba(CH₃COO)₂, BaCl₂, BaBr₂, Ba(NO₃)₂, Ba(ClO₄)₂, BaI₂, andBa(SCN)₂. Particularly preferred are NH acetate, MgCl₂, KH₂PO₄, Na₂SO₄,KCl, NaCl, and CaCl₂), such as, for example, the chloride or acetate(trifluoroacetate) salts.

Generally, peptides and variants (at least those containing peptidelinkages between amino acid residues) may be synthesized by theFmoc-polyamide mode of solid-phase peptide synthesis as disclosed byLukas et al. (Lukas et al., 1981) and by references as cited therein.Temporary N-amino group protection is afforded by the9-fluorenylmethyloxycarbonyl (Fmoc) group. Repetitive cleavage of thishighly base-labile protecting group is done using 20% piperidine in N,N-dimethylformamide. Side-chain functionalities may be protected astheir butyl ethers (in the case of serine threonine and tyrosine), butylesters (in the case of glutamic acid and aspartic acid),butyloxycarbonyl derivative (in the case of lysine and histidine),trityl derivative (in the case of cysteine) and4-methoxy-2,3,6-trimethylbenzenesulphonyl derivative (in the case ofarginine). Where glutamine or asparagine are C-terminal residues, use ismade of the 4,4′-dimethoxybenzhydryl group for protection of the sidechain amido functionalities. The solid-phase support is based on apolydimethyl-acrylamide polymer constituted from the three monomersdimethylacrylamide (backbone-monomer), bisacryloylethylene diamine(cross linker) and acryloylsarcosine methyl ester (functionalizingagent). The peptide-to-resin cleavable linked agent used is theacid-labile 4-hydroxymethyl-phenoxyacetic acid derivative. All aminoacid derivatives are added as their preformed symmetrical anhydridederivatives with the exception of asparagine and glutamine, which areadded using a reversed N,N-dicyclohexyl-carbodiimide/1hydroxybenzotriazole mediated couplingprocedure. All coupling and deprotection reactions are monitored usingninhydrin, trinitrobenzene sulphonic acid or isotin test procedures.Upon completion of synthesis, peptides are cleaved from the resinsupport with concomitant removal of side-chain protecting groups bytreatment with 95% trifluoroacetic acid containing a 50% scavenger mix.Scavengers commonly used include ethanedithiol, phenol, anisole andwater, the exact choice depending on the constituent amino acids of thepeptide being synthesized. Also a combination of solid phase andsolution phase methodologies for the synthesis of peptides is possible(see, for example, (Bruckdorfer et al., 2004), and the references ascited therein).

Trifluoroacetic acid is removed by evaporation in vacuo, with subsequenttrituration with diethyl ether affording the crude peptide. Anyscavengers present are removed by a simple extraction procedure which onlyophilization of the aqueous phase affords the crude peptide free ofscavengers. Reagents for peptide synthesis are generally available frome.g. Calbiochem-Novabiochem (Nottingham, UK).

Purification may be performed by any one, or a combination of,techniques such as re-crystallization, size exclusion chromatography,ion-exchange chromatography, hydrophobic interaction chromatography and(usually) reverse-phase high performance liquid chromatography usinge.g. acetonitrile/water gradient separation.

Analysis of peptides may be carried out using thin layer chromatography,electrophoresis, in particular capillary electrophoresis, solid phaseextraction (CSPE), reverse-phase high performance liquid chromatography,amino-acid analysis after acid hydrolysis and by fast atom bombardment(FAB) mass spectrometric analysis, as well as MALDI and ESI-Q-TOF massspectrometric analysis.

For the identification of HLA ligands by mass spectrometry, HLAmolecules from shock-frozen tissue samples were purified andHLA-associated peptides were isolated. The isolated peptides wereseparated and sequences were identified by onlinenano-electrospray-ionization (nanoESI) liquid chromatography-massspectrometry (LC-MS) experiments. The resulting peptide sequences wereverified by comparison of the fragmentation pattern of naturaltumor-associated peptides (TUMAPs) recorded from ovarian cancer samples(N≥80 samples) with the fragmentation patterns of correspondingsynthetic reference peptides of identical sequences. Since the peptideswere directly identified as ligands of HLA molecules of primary tumors,these results provide direct evidence for the natural processing andpresentation of the identified peptides on primary cancer tissueobtained from ≥80 ovarian cancer patients (cf. Example 1).

The discovery pipeline XPRESIDENT® v2.1 (see, for example, US2013-0096016, which is hereby incorporated by reference in its entirety)allows the identification and selection of relevant over-presentedpeptide vaccine candidates based on direct relative quantitation ofHLA-restricted peptide levels on cancer tissues in comparison to severaldifferent non-cancerous tissues and organs. This was achieved by thedevelopment of label-free differential quantitation using the acquiredLC-MS data processed by a proprietary data analysis pipeline, combiningalgorithms for sequence identification, spectral clustering, ioncounting, retention time alignment, charge state deconvolution andnormalization.

HLA-peptide complexes from ovarian cancer tissue samples were purifiedand HLA-associated peptides were isolated and analyzed by LC-MS (seeexample 1). All TUMAPs contained in the present application wereidentified with this approach on primary ovarian cancer samplesconfirming their presentation on primary ovarian cancer.

Besides presentation of the peptide, mRNA expression of the underlyinggene was tested. mRNA data were obtained via RNASeq analyses of normaltissues and cancer tissues (cf. Example 2, FIGS. 1A-1V). Peptides whichare derived from proteins whose coding mRNA is highly expressed incancer tissue, but very low or absent in vital normal tissues, werepreferably included in the present invention.

The present invention provides peptides that are useful in treatingcancers/tumors, preferably ovarian cancer that over- or exclusivelypresent the peptides of the invention.

These peptides were shown by mass spectrometry to be naturally presentedby HLA molecules on primary human ovarian cancer samples.

Many of the source gene/proteins (also designated “full-length proteins”or “underlying proteins”) from which the peptides are derived were shownto be highly over-expressed in cancer compared with normaltissues—“normal tissues” in relation to this invention shall mean eitherhealthy ovarian cells or other normal tissue cells, demonstrating a highdegree of tumor association of the source genes (see Example 2).Moreover, the peptides themselves are presented on tumor tissue—“tumortissue” in relation to this invention shall mean a sample from a patientsuffering from ovarian cancer.

HLA-bound peptides can be recognized by the immune system, specificallyT lymphocytes. T cells can destroy the cells presenting the recognizedHLA/peptide complex, e.g. ovarian cancer cells presenting the derivedpeptides.

The peptides of the present invention have been shown to be capable ofstimulating T cell responses and/or are over-presented and thus can beused for the production of antibodies and/or TCRs, such as soluble TCRs,according to the present invention (see Example 3, Example 4).Furthermore, the peptides when complexed with the respective MHC can beused for the production of antibodies and/or TCRs, in particular sTCRs,according to the present invention, as well. Respective methods are wellknown to the person of skill, and can be found in the respectiveliterature as well (see also below). Thus, the peptides of the presentinvention are useful for generating an immune response in a patient bywhich tumor cells can be destroyed. An immune response in a patient canbe induced by direct administration of the described peptides orsuitable precursor substances (e.g. elongated peptides, proteins, ornucleic acids encoding these peptides) to the patient, ideally incombination with an agent enhancing the immunogenicity (i.e. anadjuvant). The immune response originating from such a therapeuticvaccination can be expected to be highly specific against tumor cellsbecause the target peptides of the present invention are not presentedon normal tissues in comparable copy numbers, preventing the risk ofundesired autoimmune reactions against normal cells in the patient.

The present description further relates to T-cell receptors (TCRs)comprising an alpha chain and a beta chain (“alpha/beta TCRs”). Alsoprovided are peptides according to the invention capable of binding toTCRs and antibodies when presented by an MHC molecule.

The present description also relates to fragments of the TCRs accordingto the invention that are capable of binding to a peptide antigenaccording to the present invention when presented by an HLA molecule.The term particularly relates to soluble TCR fragments, for example TCRsmissing the transmembrane parts and/or constant regions, single chainTCRs, and fusions thereof to, for example, with lg.

The present description also relates to nucleic acids, vectors and hostcells for expressing TCRs and peptides of the present description; andmethods of using the same.

The term “T-cell receptor” (abbreviated TCR) refers to a heterodimericmolecule comprising an alpha polypeptide chain (alpha chain) and a betapolypeptide chain (beta chain), wherein the heterodimeric receptor iscapable of binding to a peptide antigen presented by an HLA molecule.The term also includes so-called gamma/delta TCRs.

In one embodiment the description provides a method of producing a TCRas described herein, the method comprising culturing a host cell capableof expressing the TCR under conditions suitable to promote expression ofthe TCR.

The description in another aspect relates to methods according to thedescription, wherein the antigen is loaded onto class I or II MHCmolecules expressed on the surface of a suitable antigen-presenting cellor artificial antigen-presenting cell by contacting a sufficient amountof the antigen with an antigen-presenting cell or the antigen is loadedonto class I or II MHC tetramers by tetramerizing the antigen/class I orII MHC complex monomers.

The alpha and beta chains of alpha/beta TCR's, and the gamma and deltachains of gamma/delta TCRs, are generally regarded as each having two“domains”, namely variable and constant domains. The variable domainconsists of a concatenation of variable region (V), and joining region(J). The variable domain may also include a leader region (L). Beta anddelta chains may also include a diversity region (D). The alpha and betaconstant domains may also include C-terminal transmembrane (TM) domainsthat anchor the alpha and beta chains to the cell membrane.

With respect to gamma/delta TCRs, the term “TCR gamma variable domain”as used herein refers to the concatenation of the TCR gamma V (TRGV)region without leader region (L), and the TCR gamma J (TRGJ) region, andthe term TCR gamma constant domain refers to the extracellular TRGCregion, or to a C-terminal truncated TRGC sequence. Likewise the term“TCR delta variable domain” refers to the concatenation of the TCR deltaV (TRDV) region without leader region (L) and the TCR delta D/J(TRDD/TRDJ) region, and the term “TCR delta constant domain” refers tothe extracellular TRDC region, or to a C-terminal truncated TRDCsequence.

TCRs of the present description preferably bind to an peptide-HLAmolecule complex with a binding affinity (KD) of about 100 μM or less,about 50 μM or less, about 25 μM or less, or about 10 μM or less. Morepreferred are high affinity TCRs having binding affinities of about 1 μMor less, about 100 nM or less, about 50 nM or less, about 25 nM or less.Non-limiting examples of preferred binding affinity ranges for TCRs ofthe present invention include about 1 nM to about 10 nM; about 10 nM toabout 20 nM; about 20 nM to about 30 nM; about 30 nM to about 40 nM;about 40 nM to about 50 nM; about 50 nM to about 60 nM; about 60 nM toabout 70 nM; about 70 nM to about 80 nM; about 80 nM to about 90 nM; andabout 90 nM to about 100 nM.

As used herein in connect with TCRs of the present description,“specific binding” and grammatical variants thereof are used to mean aTCR having a binding affinity (KD) for a peptide-HLA molecule complex of100 μM or less.

Alpha/beta heterodimeric TCRs of the present description may have anintroduced disulfide bond between their constant domains. Preferred TCRsof this type include those which have a TRAC constant domain sequenceand a TRBC1 or TRBC2 constant domain sequence except that Thr 48 of TRACand Ser 57 of TRBC1 or TRBC2 are replaced by cysteine residues, the saidcysteines forming a disulfide bond between the TRAC constant domainsequence and the TRBC1 or TRBC2 constant domain sequence of the TCR.

With or without the introduced inter-chain bond mentioned above,alpha/beta hetero-dimeric TCRs of the present description may have aTRAC constant domain sequence and a TRBC1 or TRBC2 constant domainsequence, and the TRAC constant domain sequence and the TRBC1 or TRBC2constant domain sequence of the TCR may be linked by the nativedisulfide bond between Cys4 of exon 2 of TRAC and Cys2 of exon 2 ofTRBC1 or TRBC2.

TCRs of the present description may comprise a detectable label selectedfrom the group consisting of a radionuclide, a fluorophore and biotin.TCRs of the present description may be conjugated to a therapeuticallyactive agent, such as a radionuclide, a chemotherapeutic agent, or atoxin.

In an embodiment, a TCR of the present description having at least onemutation in the alpha chain and/or having at least one mutation in thebeta chain has modified glycosylation compared to the unmutated TCR.

In an embodiment, a TCR comprising at least one mutation in the TCRalpha chain and/or TCR beta chain has a binding affinity for, and/or abinding half-life for, a peptide-HLA molecule complex, which is at leastdouble that of a TCR comprising the unmutated TCR alpha chain and/orunmutated TCR beta chain. Affinity-enhancement of tumor-specific TCRs,and its exploitation, relies on the existence of a window for optimalTCR affinities. The existence of such a window is based on observationsthat TCRs specific for HLA-A2-restricted pathogens have KD values thatare generally about 10-fold lower when compared to TCRs specific forHLA-A2-restricted tumor-associated self-antigens. It is now known,although tumor antigens have the potential to be immunogenic, becausetumors arise from the individual's own cells only mutated proteins orproteins with altered translational processing will be seen as foreignby the immune system. Antigens that are upregulated or overexpressed (socalled self-antigens) will not necessarily induce a functional immuneresponse against the tumor: T-cells expressing TCRs that are highlyreactive to these antigens will have been negatively selected within thethymus in a process known as central tolerance, meaning that onlyT-cells with low-affinity TCRs for self-antigens remain. Therefore,affinity of TCRs or variants of the present description to peptides canbe enhanced by methods well known in the art.

The present description further relates to a method of identifying andisolating a TCR according to the present description, said methodcomprising incubating PBMCs from HLA-A*02-negative healthy donors with,for example, A2/peptide monomers, incubating the PBMCs withtetramer-phycoerythrin (PE) and isolating the high avidity T-cells byfluo-rescence activated cell sorting (FACS)-Calibur analysis.

The present description further relates to a method of identifying andisolating a TCR according to the present description, said methodcomprising obtaining a transgenic mouse with the entire human TCRαβ geneloci (1.1 and 0.7 Mb), whose T-cells express a diverse human TCRrepertoire that compensates for mouse TCR deficiency, immunizing themouse with a peptide, incubating PBMCs obtained from the transgenic micewith tetramer-phycoerythrin (PE), and isolating the high avidity T-cellsby fluorescence activated cell sorting (FACS)-Calibur analysis.

In one aspect, to obtain T-cells expressing TCRs of the presentdescription, nucleic acids encoding TCR-alpha and/or TCR-beta chains ofthe present description are cloned into expression vectors, such asgamma retrovirus or lentivirus. The recombinant viruses are generatedand then tested for functionality, such as antigen specificity andfunctional avidity. An aliquot of the final product is then used totransduce the target T-cell population (generally purified from patientPBMCs), which is expanded before infusion into the patient.

In another aspect, to obtain T-cells expressing TCRs of the presentdescription, TCR RNAs are synthesized by techniques known in the art,e.g., in vitro transcription systems. The in vitro-synthesized TCR RNAsare then introduced into primary CD8+ T-cells obtained from healthydonors by electroporation to re-express tumor specific TCR-alpha and/orTCR-beta chains.

To increase the expression, nucleic acids encoding TCRs of the presentdescription may be operably linked to strong promoters, such asretroviral long terminal repeats (LTRs), cytomegalovirus (CMV), murinestem cell virus (MSCV) U3, phosphoglycerate kinase (PGK), β-actin,ubiquitin, and a simian virus 40 (SV40)/CD43 composite promoter,elongation factor (EF)-1a and the spleen focus-forming virus (SFFV)promoter. In a preferred embodiment, the promoter is heterologous to thenucleic acid being expressed.

In addition to strong promoters, TCR expression cassettes of the presentdescription may contain additional elements that can enhance transgeneexpression, including a central polypurine tract (cPPT), which promotesthe nuclear translocation of lentiviral constructs (Follenzi et al.,2000), and the woodchuck hepatitis virus posttranscriptional regulatoryelement (wPRE), which increases the level of transgene expression byincreasing RNA stability (Zufferey et al., 1999).

The alpha and beta chains of a TCR of the present invention may beencoded by nucleic acids located in separate vectors, or may be encodedby polynucleotides located in the same vector.

Achieving high-level TCR surface expression requires that both theTCR-alpha and TCR-beta chains of the introduced TCR be transcribed athigh levels. To do so, the TCR-alpha and TCR-beta chains of the presentdescription may be cloned into bi-cistronic constructs in a singlevector, which has been shown to be capable of over-coming this obstacle.The use of a viral intraribosomal entry site (IRES) between theTCR-alpha and TCR-beta chains results in the coordinated expression ofboth chains, because the TCR-alpha and TCR-beta chains are generatedfrom a single transcript that is broken into two proteins duringtranslation, ensuring that an equal molar ratio of TCR-alpha andTCR-beta chains are produced (Schmitt et al., 2009).

Nucleic acids encoding TCRs of the present description may be codonoptimized to increase expression from a host cell. Redundancy in thegenetic code allows some amino acids to be encoded by more than onecodon, but certain codons are less “op-timal” than others because of therelative availability of matching tRNAs as well as other factors(Gustafsson et al., 2004). Modifying the TCR-alpha and TCR-beta genesequences such that each amino acid is encoded by the optimal codon formammalian gene expression, as well as eliminating mRNA instabilitymotifs or cryptic splice sites, has been shown to significantly enhanceTCR-alpha and TCR-beta gene expression (Scholten et al., 2006).

Furthermore, mispairing between the introduced and endogenous TCR chainsmay result in the acquisition of specificities that pose a significantrisk for autoimmunity. For example, the formation of mixed TCR dimersmay reduce the number of CD3 molecules available to form properly pairedTCR complexes, and therefore can significantly decrease the functionalavidity of the cells expressing the introduced TCR (Kuball et al.,2007).

To reduce mispairing, the C-terminus domain of the introduced TCR chainsof the present description may be modified in order to promoteinterchain affinity, while de-creasing the ability of the introducedchains to pair with the endogenous TCR. These strategies may includereplacing the human TCR-alpha and TCR-beta C-terminus domains with theirmurine counterparts (murinized C-terminus domain); generating a secondinterchain disulfide bond in the C-terminus domain by introducing asecond cysteine residue into both the TCR-alpha and TCR-beta chains ofthe introduced TCR (cysteine modification); swapping interactingresidues in the TCR-alpha and TCR-beta chain C-terminus domains(“knob-in-hole”); and fusing the variable domains of the TCR-alpha andTCR-beta chains directly to CD3ζ (CD3ζ fusion) (Schmitt et al., 2009).

In an embodiment, a host cell is engineered to express a TCR of thepresent description. In preferred embodiments, the host cell is a humanT-cell or T-cell progenitor. In some embodiments the T-cell or T-cellprogenitor is obtained from a cancer patient. In other embodiments theT-cell or T-cell progenitor is obtained from a healthy donor. Host cellsof the present description can be allogeneic or autologous with respectto a patient to be treated. In one embodiment, the host is a gamma/deltaT-cell transformed to express an alpha/beta TCR.

A “pharmaceutical composition” is a composition suitable foradministration to a human being in a medical setting. Preferably, apharmaceutical composition is sterile and produced according to GMPguidelines.

The pharmaceutical compositions comprise the peptides either in the freeform or in the form of a pharmaceutically acceptable salt (see alsoabove). As used herein, “a pharmaceutically acceptable salt” refers to aderivative of the disclosed peptides wherein the peptide is modified bymaking acid or base salts of the agent. For example, acid salts areprepared from the free base (typically wherein the neutral form of thedrug has a neutral —NH2 group) involving reaction with a suitable acid.Suitable acids for preparing acid salts include both organic acids,e.g., acetic acid, propionic acid, glycolic acid, pyruvic acid, oxalicacid, malic acid, malonic acid, succinic acid, maleic acid, fumaricacid, tartaric acid, citric acid, benzoic acid, cinnamic acid, mandelicacid, methane sulfonic acid, ethane sulfonic acid, p-toluenesulfonicacid, salicylic acid, and the like, as well as inorganic acids, e.g.,hydrochloric acid, hydrobromic acid, sulfuric acid, nitric acidphosphoric acid and the like. Conversely, preparation of basic salts ofacid moieties which may be present on a peptide are prepared using apharmaceutically acceptable base such as sodium hydroxide, potassiumhydroxide, ammonium hydroxide, calcium hydroxide, trimethylamine or thelike.

In an especially preferred embodiment, the pharmaceutical compositionscomprise the peptides as salts of acetic acid (acetates), trifluoroacetates or hydrochloric acid (chlorides).

Preferably, the medicament of the present invention is animmunotherapeutic such as a vaccine. It may be administered directlyinto the patient, into the affected organ or systemically i.d., i.m.,s.c., i.p. and i.v., or applied ex vivo to cells derived from thepatient or a human cell line which are subsequently administered to thepatient, or used in vitro to select a subpopulation of immune cellsderived from the patient, which are then re-administered to the patient.If the nucleic acid is administered to cells in vitro, it may be usefulfor the cells to be transfected so as to co-express immune-stimulatingcytokines, such as interleukin-2. The peptide may be substantially pure,or combined with an immune-stimulating adjuvant (see below) or used incombination with immune-stimulatory cytokines, or be administered with asuitable delivery system, for example liposomes. The peptide may also beconjugated to a suitable carrier such as keyhole limpet haemocyanin(KLH) or mannan (see WO 95/18145 and (Longenecker et al., 1993)). Thepeptide may also be tagged, may be a fusion protein, or may be a hybridmolecule. The peptides whose sequence is given in the present inventionare expected to stimulate CD4 or CD8 T cells. However, stimulation ofCD8 T cells is more efficient in the presence of help provided by CD4T-helper cells. Thus, for MHC Class I epitopes that stimulate CD8 Tcells the fusion partner or sections of a hybrid molecule suitablyprovide epitopes which stimulate CD4-positive T cells. CD4- andCD8-stimulating epitopes are well known in the art and include thoseidentified in the present invention.

In one aspect, the vaccine comprises at least one peptide having theamino acid sequence set forth SEQ ID No. 1 to SEQ ID No. 772, and atleast one additional peptide, preferably two to 50, more preferably twoto 25, even more preferably two to 20 and most preferably two, three,four, five, six, seven, eight, nine, ten, eleven, twelve, thirteen,fourteen, fifteen, sixteen, seventeen or eighteen peptides. Thepeptide(s) may be derived from one or more specific TAAs and may bind toMHC class I molecules.

A further aspect of the invention provides a nucleic acid (for example apolynucleotide) encoding a peptide or peptide variant of the invention.The polynucleotide may be, for example, DNA, cDNA, PNA, RNA orcombinations thereof, either single- and/or double-stranded, or nativeor stabilized forms of polynucleotides, such as, for example,polynucleotides with a phosphorothioate backbone and it may or may notcontain introns so long as it codes for the peptide. Of course, onlypeptides that contain naturally occurring amino acid residues joined bynaturally occurring peptide bonds are encodable by a polynucleotide. Astill further aspect of the invention provides an expression vectorcapable of expressing a polypeptide according to the invention.

A variety of methods have been developed to link polynucleotides,especially DNA, to vectors for example via complementary cohesivetermini. For instance, complementary homopolymer tracts can be added tothe DNA segment to be inserted to the vector DNA. The vector and DNAsegment are then joined by hydrogen bonding between the complementaryhomopolymeric tails to form recombinant DNA molecules.

Synthetic linkers containing one or more restriction sites provide analternative method of joining the DNA segment to vectors. Syntheticlinkers containing a variety of restriction endonuclease sites arecommercially available from a number of sources including InternationalBiotechnologies Inc. New Haven, Conn., USA.

A desirable method of modifying the DNA encoding the polypeptide of theinvention employs the polymerase chain reaction as disclosed by Saiki RK, et al. (Saiki et al., 1988). This method may be used for introducingthe DNA into a suitable vector, for example by engineering in suitablerestriction sites, or it may be used to modify the DNA in other usefulways as is known in the art. If viral vectors are used, pox- oradenovirus vectors are preferred.

The DNA (or in the case of retroviral vectors, RNA) may then beexpressed in a suitable host to produce a polypeptide comprising thepeptide or variant of the invention. Thus, the DNA encoding the peptideor variant of the invention may be used in accordance with knowntechniques, appropriately modified in view of the teachings containedherein, to construct an expression vector, which is then used totransform an appropriate host cell for the expression and production ofthe polypeptide of the invention. Such techniques include thosedisclosed, for example, in U.S. Pat. Nos. 4,440,859, 4,530,901,4,582,800, 4,677,063, 4,678,751, 4,704,362, 4,710,463, 4,757,006,4,766,075, and 4,810,648.

The DNA (or in the case of retroviral vectors, RNA) encoding thepolypeptide constituting the compound of the invention may be joined toa wide variety of other DNA sequences for introduction into anappropriate host. The companion DNA will depend upon the nature of thehost, the manner of the introduction of the DNA into the host, andwhether episomal maintenance or integration is desired.

Generally, the DNA is inserted into an expression vector, such as aplasmid, in proper orientation and correct reading frame for expression.If necessary, the DNA may be linked to the appropriate transcriptionaland translational regulatory control nucleotide sequences recognized bythe desired host, although such controls are generally available in theexpression vector. The vector is then introduced into the host throughstandard techniques. Generally, not all of the hosts will be transformedby the vector. Therefore, it will be necessary to select for transformedhost cells. One selection technique involves incorporating into theexpression vector a DNA sequence, with any necessary control elements,that codes for a selectable trait in the transformed cell, such asantibiotic resistance.

Alternatively, the gene for such selectable trait can be on anothervector, which is used to co-transform the desired host cell.

Host cells that have been transformed by the recombinant DNA of theinvention are then cultured for a sufficient time and under appropriateconditions known to those skilled in the art in view of the teachingsdisclosed herein to permit the expression of the polypeptide, which canthen be recovered.

Many expression systems are known, including bacteria (for example E.coli and Bacillus subtilis), yeasts (for example Saccharomycescerevisiae), filamentous fungi (for example Aspergillus spec.), plantcells, animal cells and insect cells. Preferably, the system can bemammalian cells such as CHO cells available from the ATCC Cell BiologyCollection.

A typical mammalian cell vector plasmid for constitutive expressioncomprises the CMV or SV40 promoter with a suitable poly A tail and aresistance marker, such as neomycin. One example is pSVL available fromPharmacia, Piscataway, N.J., USA. An example of an inducible mammalianexpression vector is pMSG, also available from Pharmacia. Useful yeastplasmid vectors are pRS403-406 and pRS413-416 and are generallyavailable from Stratagene Cloning Systems, La Jolla, Calif. 92037, USA.Plasmids pRS403, pRS404, pRS405 and pRS406 are Yeast Integratingplasmids (YIps) and incorporate the yeast selectable markers HIS3, TRP1,LEU2 and URA3. Plasmids pRS413-416 are Yeast Centromere plasmids (Ycps).CMV promoter-based vectors (for example from Sigma-Aldrich) providetransient or stable expression, cytoplasmic expression or secretion, andN-terminal or C-terminal tagging in various combinations of FLAG,3×FLAG, c-myc or MAT. These fusion proteins allow for detection,purification and analysis of recombinant protein. Dual-tagged fusionsprovide flexibility in detection.

The strong human cytomegalovirus (CMV) promoter regulatory region drivesconstitutive protein expression levels as high as 1 mg/L in COS cells.For less potent cell lines, protein levels are typically ˜0.1 mg/L. Thepresence of the SV40 replication origin will result in high levels ofDNA replication in SV40 replication permissive COS cells. CMV vectors,for example, can contain the pMB1 (derivative of pBR322) origin forreplication in bacterial cells, the b-lactamase gene for ampicillinresistance selection in bacteria, hGH polyA, and the f1 origin. Vectorscontaining the pre-pro-trypsin leader (PPT) sequence can direct thesecretion of FLAG fusion proteins into the culture medium forpurification using ANTI-FLAG antibodies, resins, and plates. Othervectors and expression systems are well known in the art for use with avariety of host cells.

In another embodiment two or more peptides or peptide variants of theinvention are encoded and thus expressed in a successive order (similarto “beads on a string” constructs). In doing so, the peptides or peptidevariants may be linked or fused together by stretches of linker aminoacids, such as for example LLLLLL, or may be linked without anyadditional peptide(s) between them. These constructs can also be usedfor cancer therapy, and may induce immune responses both involving MHC Iand MHC II.

The present invention also relates to a host cell transformed with apolynucleotide vector construct of the present invention. The host cellcan be either prokaryotic or eukaryotic. Bacterial cells may bepreferred prokaryotic host cells in some circumstances and typically area strain of E. coli such as, for example, the E. coli strains DH5available from Bethesda Research Laboratories Inc., Bethesda, Md., USA,and RR1 available from the American Type Culture Collection (ATCC) ofRockville, Md., USA (No ATCC 31343). Preferred eukaryotic host cellsinclude yeast, insect and mammalian cells, preferably vertebrate cellssuch as those from a mouse, rat, monkey or human fibroblastic and coloncell lines. Yeast host cells include YPH499, YPH500 and YPH501, whichare generally available from Stratagene Cloning Systems, La Jolla,Calif. 92037, USA. Preferred mammalian host cells include Chinesehamster ovary (CHO) cells available from the ATCC as CCL61, NIH Swissmouse embryo cells NIH/3T3 available from the ATCC as CRL 1658, monkeykidney-derived COS-1 cells available from the ATCC as CRL 1650 and 293cells which are human embryonic kidney cells. Preferred insect cells areSf9 cells which can be transfected with baculovirus expression vectors.An overview regarding the choice of suitable host cells for expressioncan be found in, for example, the textbook of Paulina Balbás and ArgeliaLorence “Methods in Molecular Biology Recombinant Gene Expression,Reviews and Protocols,” Part One, Second Edition, ISBN978-1-58829-262-9, and other literature known to the person of skill.

Transformation of appropriate cell hosts with a DNA construct of thepresent invention is accomplished by well-known methods that typicallydepend on the type of vector used. With regard to transformation ofprokaryotic host cells, see, for example, Cohen et al. (Cohen et al.,1972) and (Green and Sambrook, 2012). Transformation of yeast cells isdescribed in Sherman et al. (Sherman et al., 1986). The method of Beggs(Beggs, 1978) is also useful. With regard to vertebrate cells, reagentsuseful in transfecting such cells, for example calcium phosphate andDEAE-dextran or liposome formulations, are available from StratageneCloning Systems, or Life Technologies Inc., Gaithersburg, Md. 20877,USA. Electroporation is also useful for transforming and/or transfectingcells and is well known in the art for transforming yeast cell,bacterial cells, insect cells and vertebrate cells.

Successfully transformed cells, i.e. cells that contain a DNA constructof the present invention, can be identified by well-known techniquessuch as PCR. Alternatively, the presence of the protein in thesupernatant can be detected using antibodies.

It will be appreciated that certain host cells of the invention areuseful in the preparation of the peptides of the invention, for examplebacterial, yeast and insect cells. However, other host cells may beuseful in certain therapeutic methods. For example, antigen-presentingcells, such as dendritic cells, may usefully be used to express thepeptides of the invention such that they may be loaded into appropriateMHC molecules. Thus, the current invention provides a host cellcomprising a nucleic acid or an expression vector according to theinvention.

In a preferred embodiment the host cell is an antigen presenting cell,in particular a dendritic cell or antigen presenting cell. APCs loadedwith a recombinant fusion protein containing prostatic acid phosphatase(PAP) were approved by the U.S. Food and Drug Administration (FDA) onApr. 29, 2010, to treat asymptomatic or minimally symptomatic metastaticHRPC (Sipuleucel-T) (Rini et al., 2006; Small et al., 2006).

A further aspect of the invention provides a method of producing apeptide or its variant, the method comprising culturing a host cell andisolating the peptide from the host cell or its culture medium.

In another embodiment, the peptide, the nucleic acid or the expressionvector of the invention are used in medicine. For example, the peptideor its variant may be prepared for intravenous (i.v.) injection,sub-cutaneous (s.c.) injection, intradermal (i.d.) injection,intraperitoneal (i.p.) injection, intramuscular (i.m.) injection.Preferred methods of peptide injection include s.c., i.d., i.p., i.m.,and i.v. Preferred methods of DNA injection include i.d., i.m., s.c.,i.p. and i.v. Doses of e.g. between 50 μg and 1.5 mg, preferably 125 μgto 500 μg, of peptide or DNA may be given and will depend on therespective peptide or DNA. Dosages of this range were successfully usedin previous trials (Walter et al., 2012).

The polynucleotide used for active vaccination may be substantiallypure, or contained in a suitable vector or delivery system. The nucleicacid may be DNA, cDNA, PNA, RNA or a combination thereof. Methods fordesigning and introducing such a nucleic acid are well known in the art.An overview is provided by e.g. Teufel et al. (Teufel et al., 2005).Polynucleotide vaccines are easy to prepare, but the mode of action ofthese vectors in inducing an immune response is not fully understood.Suitable vectors and delivery systems include viral DNA and/or RNA, suchas systems based on adenovirus, vaccinia virus, retroviruses, herpesvirus, adeno-associated virus or hybrids containing elements of morethan one virus. Non-viral delivery systems include cationic lipids andcationic polymers and are well known in the art of DNA delivery.Physical delivery, such as via a “gene-gun” may also be used. Thepeptide or peptides encoded by the nucleic acid may be a fusion protein,for example with an epitope that stimulates T cells for the respectiveopposite CDR as noted above.

The medicament of the invention may also include one or more adjuvants.Adjuvants are substances that non-specifically enhance or potentiate theimmune response (e.g., immune responses mediated by CD8-positive T cellsand helper-T (TH) cells to an antigen, and would thus be considereduseful in the medicament of the present invention. Suitable adjuvantsinclude, but are not limited to, 1018 ISS, aluminum salts, AMPLIVAX®,AS15, BCG, CP-870,893, CpG7909, CyaA, dSLIM, flagellin or TLRS ligandsderived from flagellin, FLT3 ligand, GM-CSF, IC30, IC31, Imiquimod(ALDARA®), resiquimod, ImuFact IMP321, Interleukins as IL-2, IL-13,IL-21, Interferon-alpha or -beta, or pegylated derivatives thereof, ISPatch, ISS, ISCOMATRIX, ISCOMs, JuvImmune®, LipoVac, MALP2, MF59,monophosphoryl lipid A, Montanide IMS 1312, Montanide ISA 206, MontanideISA 50V, Montanide ISA-51, water-in-oil and oil-in-water emulsions,OK-432, OM-174, OM-197-MP-EC, ONTAK, OspA, PepTel® vector system,poly(lactid co-glycolid) [PLG]-based and dextran microparticles,talactoferrin SRL172, Virosomes and other Virus-like particles, YF-17D,VEGF trap, R848, beta-glucan, Pam3Cys, Aquila's QS21 stimulon, which isderived from saponin, mycobacterial extracts and synthetic bacterialcell wall mimics, and other proprietary adjuvants such as Ribi's Detox,Quil, or Superfos. Adjuvants such as Freund's or GM-CSF are preferred.Several immunological adjuvants (e.g., MF59) specific for dendriticcells and their preparation have been described previously (Allison andKrummel, 1995). Also cytokines may be used. Several cytokines have beendirectly linked to influencing dendritic cell migration to lymphoidtissues (e.g., TNF-), accelerating the maturation of dendritic cellsinto efficient antigen-presenting cells for T-lymphocytes (e.g., GM-CSF,IL-1 and IL-4) (U.S. Pat. No. 5,849,589, specifically incorporatedherein by reference in its entirety) and acting as immunoadjuvants(e.g., IL-12, IL-15, IL-23, IL-7, IFN-alpha. IFN-beta) (Gabrilovich etal., 1996).

CpG immunostimulatory oligonucleotides have also been reported toenhance the effects of adjuvants in a vaccine setting. Without beingbound by theory, CpG oligonucleotides act by activating the innate(non-adaptive) immune system via Toll-like receptors (TLR), mainly TLR9.CpG triggered TLR9 activation enhances antigen-specific humoral andcellular responses to a wide variety of antigens, including peptide orprotein antigens, live or killed viruses, dendritic cell vaccines,autologous cellular vaccines and polysaccharide conjugates in bothprophylactic and therapeutic vaccines. More importantly it enhancesdendritic cell maturation and differentiation, resulting in enhancedactivation of TH1 cells and strong cytotoxic T-lymphocyte (CTL)generation, even in the absence of CD4 T cell help. The TH1 bias inducedby TLR9 stimulation is maintained even in the presence of vaccineadjuvants such as alum or incomplete Freund's adjuvant (IFA) thatnormally promote a TH2 bias. CpG oligonucleotides show even greateradjuvant activity when formulated or co-administered with otheradjuvants or in formulations such as microparticles, nanoparticles,lipid emulsions or similar formulations, which are especially necessaryfor inducing a strong response when the antigen is relatively weak. Theyalso accelerate the immune response and enable the antigen doses to bereduced by approximately two orders of magnitude, with comparableantibody responses to the full-dose vaccine without CpG in someexperiments (Krieg, 2006). U.S. Pat. No. 6,406,705 B1 describes thecombined use of CpG oligonucleotides, non-nucleic acid adjuvants and anantigen to induce an antigen-specific immune response. A CpG TLR9antagonist is dSLIM (double Stem Loop Immunomodulator) by Mologen(Berlin, Germany) which is a preferred component of the pharmaceuticalcomposition of the present invention. Other TLR binding molecules suchas RNA binding TLR 7, TLR 8 and/or TLR 9 may also be used.

Other examples for useful adjuvants include, but are not limited tochemically modified CpGs (e.g. CpR, Idera), dsRNA analogues such asPoly(I:C) and derivates thereof (e.g. AmpliGen®, Hiltonol®, poly-(ICLC),poly(IC-R), poly(I:C12U), non-CpG bacterial DNA or RNA as well asimmunoactive small molecules and antibodies such as cyclophosphamide,sunitinib, Bevacizumab®, celebrex, NCX-4016, sildenafil, tadalafil,vardenafil, sorafenib, temozolomide, temsirolimus, XL-999, CP-547632,pazopanib, VEGF Trap, ZD2171, AZD2171, anti-CTLA4, other antibodiestargeting key structures of the immune system (e.g. anti-CD40,anti-TGFbeta, anti-TNFalpha receptor) and SC58175, which may acttherapeutically and/or as an adjuvant. The amounts and concentrations ofadjuvants and additives useful in the context of the present inventioncan readily be determined by the skilled artisan without undueexperimentation.

Preferred adjuvants are anti-CD40, imiquimod, resiquimod, GM-CSF,cyclophosphamide, sunitinib, bevacizumab, interferon-alpha, CpGoligonucleotides and derivates, poly-(I:C) and derivates, RNA,sildenafil, and particulate formulations with PLG or virosomes.

In a preferred embodiment, the pharmaceutical composition according tothe invention the adjuvant is selected from the group consisting ofcolony-stimulating factors, such as Granulocyte Macrophage ColonyStimulating Factor (GM-CSF, sargramostim), cyclophosphamide, imiquimod,resiquimod, and interferon-alpha.

In a preferred embodiment, the pharmaceutical composition according tothe invention the adjuvant is selected from the group consisting ofcolony-stimulating factors, such as Granulocyte Macrophage ColonyStimulating Factor (GM-CSF, sargramostim), cyclophosphamide, imiquimodand resiquimod. In a preferred embodiment of the pharmaceuticalcomposition according to the invention, the adjuvant iscyclophosphamide, imiquimod or resiquimod. Even more preferred adjuvantsare Montanide IMS 1312, Montanide ISA 206, Montanide ISA 50V, MontanideISA-51, poly-ICLC (Hiltonol®) and anti-CD40 mAB, or combinationsthereof.

This composition is used for parenteral administration, such assubcutaneous, intradermal, intramuscular or oral administration. Forthis, the peptides and optionally other molecules are dissolved orsuspended in a pharmaceutically acceptable, preferably aqueous carrier.In addition, the composition can contain excipients, such as buffers,binding agents, blasting agents, diluents, flavors, lubricants, etc. Thepeptides can also be administered together with immune stimulatingsubstances, such as cytokines. An extensive listing of excipients thatcan be used in such a composition, can be, for example, taken from A.Kibbe, Handbook of Pharmaceutical Excipients (Kibbe, 2000). Thecomposition can be used for a prevention, prophylaxis and/or therapy ofadenomatous or cancerous diseases. Exemplary formulations can be foundin, for example, EP2112253.

It is important to realize that the immune response triggered by thevaccine according to the invention attacks the cancer in differentcell-stages and different stages of development. Furthermore differentcancer associated signaling pathways are attacked. This is an advantageover vaccines that address only one or few targets, which may cause thetumor to easily adapt to the attack (tumor escape). Furthermore, not allindividual tumors express the same pattern of antigens. Therefore, acombination of several tumor-associated peptides ensures that everysingle tumor bears at least some of the targets. The composition isdesigned in such a way that each tumor is expected to express several ofthe antigens and cover several independent pathways necessary for tumorgrowth and maintenance. Thus, the vaccine can easily be used“off-the-shelf” for a larger patient population. This means that apre-selection of patients to be treated with the vaccine can berestricted to HLA typing, does not require any additional biomarkerassessments for antigen expression, but it is still ensured that severaltargets are simultaneously attacked by the induced immune response,which is important for efficacy (Banchereau et al., 2001; Walter et al.,2012).

As used herein, the term “scaffold” refers to a molecule thatspecifically binds to an (e.g. antigenic) determinant. In oneembodiment, a scaffold is able to direct the entity to which it isattached (e.g. a (second) antigen binding moiety) to a target site, forexample to a specific type of tumor cell or tumor stroma bearing theantigenic determinant (e.g. the complex of a peptide with MHC, accordingto the application at hand). In another embodiment a scaffold is able toactivate signaling through its target antigen, for example a T cellreceptor complex antigen. Scaffolds include but are not limited toantibodies and fragments thereof, antigen binding domains of anantibody, comprising an antibody heavy chain variable region and anantibody light chain variable region, binding proteins comprising atleast one ankyrin repeat motif and single domain antigen binding (SDAB)molecules, aptamers, (soluble) TCRs and (modified) cells such asallogenic or autologous T cells. To assess whether a molecule is ascaffold binding to a target, binding assays can be performed.

“Specific” binding means that the scaffold binds the peptide-MHC-complexof interest better than other naturally occurring peptide-MHC-complexes,to an extent that a scaffold armed with an active molecule that is ableto kill a cell bearing the specific target is not able to kill anothercell without the specific target but presenting other peptide-MHCcomplex(es). Binding to other peptide-MHC complexes is irrelevant if thepeptide of the cross-reactive peptide-MHC is not naturally occurring,i.e. not derived from the human HLA-peptidome. Tests to assess targetcell killing are well known in the art. They should be performed usingtarget cells (primary cells or cell lines) with unaltered peptide-MHCpresentation, or cells loaded with peptides such that naturallyoccurring peptide-MHC levels are reached.

Each scaffold can comprise a labelling which provides that the boundscaffold can be detected by determining the presence or absence of asignal provided by the label. For example, the scaffold can be labelledwith a fluorescent dye or any other applicable cellular marker molecule.Such marker molecules are well known in the art. For example afluorescence-labelling, for example provided by a fluorescence dye, canprovide a visualization of the bound aptamer by fluorescence or laserscanning microscopy or flow cytometry.

Each scaffold can be conjugated with a second active molecule such asfor example IL-21, anti-CD3, and anti-CD28. For further information onpolypeptide scaffolds see for example the background section of WO2014/071978A1 and the references cited therein.

The present invention further relates to aptamers. Aptamers (see forexample WO 2014/191359 and the literature as cited therein) are shortsingle-stranded nucleic acid molecules, which can fold into definedthree-dimensional structures and recognize specific target structures.They have appeared to be suitable alternatives for developing targetedtherapies. Aptamers have been shown to selectively bind to a variety ofcomplex targets with high affinity and specificity.

Aptamers recognizing cell surface located molecules have been identifiedwithin the past decade and provide means for developing diagnostic andtherapeutic approaches. Since aptamers have been shown to possess almostno toxicity and immunogenicity they are promising candidates forbiomedical applications. Indeed aptamers, for example prostate-specificmembrane-antigen recognizing aptamers, have been successfully employedfor targeted therapies and shown to be functional in xenograft in vivomodels. Furthermore, aptamers recognizing specific tumor cell lines havebeen identified.

DNA aptamers can be selected to reveal broad-spectrum recognitionproperties for various cancer cells, and particularly those derived fromsolid tumors, while non-tumorigenic and primary healthy cells are notrecognized. If the identified aptamers recognize not only a specifictumor sub-type but rather interact with a series of tumors, this rendersthe aptamers applicable as so-called broad-spectrum diagnostics andtherapeutics.

Further, investigation of cell-binding behavior with flow cytometryshowed that the aptamers revealed very good apparent affinities that arewithin the nanomolar range.

Aptamers are useful for diagnostic and therapeutic purposes. Further, itcould be shown that some of the aptamers are taken up by tumor cells andthus can function as molecular vehicles for the targeted delivery ofanti-cancer agents such as si RNA into tumor cells.

Aptamers can be selected against complex targets such as cells andtissues and complexes of the peptides comprising, preferably consistingof, a sequence according to any of SEQ ID NO 1 to SEQ ID NO 772,according to the invention at hand with the MHC molecule, using thecell-SELEX (Systematic Evolution of Ligands by Exponential enrichment)technique.

The peptides of the present invention can be used to generate anddevelop specific antibodies against MHC/peptide complexes. These can beused for therapy, targeting toxins or radioactive substances to thediseased tissue. Another use of these antibodies can be targetingradionuclides to the diseased tissue for imaging purposes such as PET.This use can help to detect small metastases or to determine the sizeand precise localization of diseased tissues.

Therefore, it is a further aspect of the invention to provide a methodfor producing a recombinant antibody specifically binding to a humanmajor histocompatibility complex (MHC) class I or II being complexedwith a HLA-restricted antigen (preferably a peptide according to thepresent invention), the method comprising: immunizing a geneticallyengineered non-human mammal comprising cells expressing said human majorhistocompatibility complex (MHC) class I or II with a soluble form of aMHC class I or II molecule being complexed with said HLA-restrictedantigen; isolating mRNA molecules from antibody producing cells of saidnon-human mammal; producing a phage display library displaying proteinmolecules encoded by said mRNA molecules; and isolating at least onephage from said phage display library, said at least one phagedisplaying said antibody specifically binding to said human majorhistocompatibility complex (MHC) class I or II being complexed with saidHLA-restricted antigen.

It is thus a further aspect of the invention to provide an antibody thatspecifically binds to a human major histocompatibility complex (MHC)class I or II being complexed with a HLA-restricted antigen, wherein theantibody preferably is a polyclonal antibody, monoclonal antibody,bi-specific antibody and/or a chimeric antibody.

Respective methods for producing such antibodies and single chain classI major histocompatibility complexes, as well as other tools for theproduction of these antibodies are disclosed in WO 03/068201, WO2004/084798, WO 01/72768, WO 03/070752, and in publications (Cohen etal., 2003a; Cohen et al., 2003b; Denkberg et al., 2003), which for thepurposes of the present invention are all explicitly incorporated byreference in their entireties.

Preferably, the antibody is binding with a binding affinity of below 20nanomolar, preferably of below 10 nanomolar, to the complex, which isalso regarded as “specific” in the context of the present invention.

The present invention relates to a peptide comprising a sequence that isselected from the group consisting of SEQ ID NO: 1 to SEQ ID NO: 772, ora variant thereof which is at least 88% homologous (preferablyidentical) to SEQ ID NO: 1 to SEQ ID NO: 772 or a variant thereof thatinduces T cells cross-reacting with said peptide, wherein said peptideis not the underlying full-length polypeptide.

The present invention further relates to a peptide comprising a sequencethat is selected from the group consisting of SEQ ID NO: 1 to SEQ ID NO:772 or a variant thereof which is at least 88% homologous (preferablyidentical) to SEQ ID NO: 1 to SEQ ID NO: 772, wherein said peptide orvariant has an overall length of between 8 and 100, preferably between 8and 30, and most preferred between 8 and 14 amino acids.

The present invention further relates to the peptides according to theinvention that have the ability to bind to a molecule of the human majorhistocompatibility complex (MHC) class-I or -II.

The present invention further relates to the peptides according to theinvention wherein the peptide consists or consists essentially of anamino acid sequence according to SEQ ID NO: 1 to SEQ ID NO: 772.

The present invention further relates to the peptides according to theinvention, wherein the peptide is (chemically) modified and/or includesnon-peptide bonds.

The present invention further relates to the peptides according to theinvention, wherein the peptide is part of a fusion protein, inparticular comprising N-terminal amino acids of the HLA-DRantigen-associated invariant chain (Ii), or wherein the peptide is fusedto (or into) an antibody, such as, for example, an antibody that isspecific for dendritic cells.

The present invention further relates to a nucleic acid, encoding thepeptides according to the invention, provided that the peptide is notthe complete (full) human protein.

The present invention further relates to the nucleic acid according tothe invention that is DNA, cDNA, PNA, RNA or combinations thereof.

The present invention further relates to an expression vector capable ofexpressing a nucleic acid according to the present invention.

The present invention further relates to a peptide according to thepresent invention, a nucleic acid according to the present invention oran expression vector according to the present invention for use inmedicine, in particular in the treatment of ovarian cancer.

The present invention further relates to a host cell comprising anucleic acid according to the invention or an expression vectoraccording to the invention.

The present invention further relates to the host cell according to thepresent invention that is an antigen presenting cell, and preferably adendritic cell.

The present invention further relates to a method of producing a peptideaccording to the present invention, said method comprising culturing thehost cell according to the present invention, and isolating the peptidefrom said host cell or its culture medium.

The present invention further relates to the method according to thepresent invention, where-in the antigen is loaded onto class I or II MHCmolecules expressed on the surface of a suitable antigen-presenting cellby contacting a sufficient amount of the antigen with anantigen-presenting cell.

The present invention further relates to the method according to theinvention, wherein the antigen-presenting cell comprises an expressionvector capable of expressing said peptide containing SEQ ID NO: 1 to SEQID NO: 772 or said variant amino acid sequence.

The present invention further relates to activated T cells, produced bythe method according to the present invention, wherein said T cellsselectively recognizes a cell which aberrantly expresses a polypeptidecomprising an amino acid sequence according to the present invention.

The present invention further relates to a method of killing targetcells in a patient which target cells aberrantly express a polypeptidecomprising any amino acid sequence according to the present invention,the method comprising administering to the patient an effective numberof T cells as according to the present invention.

The present invention further relates to the use of any peptidedescribed, a nucleic acid according to the present invention, anexpression vector according to the present invention, a cell accordingto the present invention, or an activated cytotoxic T lymphocyteaccording to the present invention as a medicament or in the manufactureof a medicament. The present invention further relates to a useaccording to the present invention, wherein the medicament is activeagainst cancer.

The present invention further relates to a use according to theinvention, wherein the medicament is a vaccine. The present inventionfurther relates to a use according to the invention, wherein themedicament is active against cancer.

The present invention further relates to a use according to theinvention, wherein said cancer cells are ovarian cancer cells or othersolid or hematological tumor cells such as hepatocellular carcinoma,colorectal carcinoma, glioblastoma, gastric cancer, esophageal cancer,non-small cell lung cancer, small cell lung cancer, pancreatic cancer,renal cell carcinoma, prostate cancer, melanoma, breast cancer, chroniclymphocytic leukemia, Non-Hodgkin lymphoma, acute myeloid leukemia,gallbladder cancer and cholangiocarcinoma, urinary bladder cancer,uterine cancer, head and neck squamous cell carcinoma, mesothelioma.

The present invention further relates to particular marker proteins andbiomarkers based on the peptides according to the present invention,herein called “targets” that can be used in the diagnosis and/orprognosis of ovarian cancer. The present invention also relates to theuse of these novel targets for cancer treatment.

The term “antibody” or “antibodies” is used herein in a broad sense andincludes both polyclonal and monoclonal antibodies. In addition tointact or “full” immunoglobulin molecules, also included in the term“antibodies” are fragments (e.g. CDRs, Fv, Fab and Fc fragments) orpolymers of those immunoglobulin molecules and humanized versions ofimmunoglobulin molecules, as long as they exhibit any of the desiredproperties (e.g., specific binding of a ovarian cancer marker(poly)peptide, delivery of a toxin to a ovarian cancer cell expressing acancer marker gene at an increased level, and/or inhibiting the activityof a ovarian cancer marker polypeptide) according to the invention.

Whenever possible, the antibodies of the invention may be purchased fromcommercial sources. The antibodies of the invention may also begenerated using well-known methods. The skilled artisan will understandthat either full length ovarian cancer marker polypeptides or fragmentsthereof may be used to generate the antibodies of the invention. Apolypeptide to be used for generating an antibody of the invention maybe partially or fully purified from a natural source, or may be producedusing recombinant DNA techniques.

For example, a cDNA encoding a peptide according to the presentinvention, such as a peptide according to SEQ ID NO: 1 to SEQ ID NO: 772polypeptide, or a variant or fragment thereof, can be expressed inprokaryotic cells (e.g., bacteria) or eukaryotic cells (e.g., yeast,insect, or mammalian cells), after which the recombinant protein can bepurified and used to generate a monoclonal or polyclonal antibodypreparation that specifically bind the ovarian cancer marker polypeptideused to generate the antibody according to the invention.

One of skill in the art will realize that the generation of two or moredifferent sets of monoclonal or polyclonal antibodies maximizes thelikelihood of obtaining an antibody with the specificity and affinityrequired for its intended use (e.g., ELISA, immunohistochemistry, invivo imaging, immunotoxin therapy). The antibodies are tested for theirdesired activity by known methods, in accordance with the purpose forwhich the antibodies are to be used (e.g., ELISA, immunohistochemistry,immunotherapy, etc.; for further guidance on the generation and testingof antibodies, see, e.g., Greenfield, 2014 (Greenfield, 2014)). Forexample, the antibodies may be tested in ELISA assays or, Western blots,immunohistochemical staining of formalin-fixed cancers or frozen tissuesections. After their initial in vitro characterization, antibodiesintended for therapeutic or in vivo diagnostic use are tested accordingto known clinical testing methods.

The term “monoclonal antibody” as used herein refers to an antibodyobtained from a substantially homogeneous population of antibodies,i.e.; the individual antibodies comprising the population are identicalexcept for possible naturally occurring mutations that may be present inminor amounts. The monoclonal antibodies herein specifically include“chimeric” antibodies in which a portion of the heavy and/or light chainis identical with or homologous to corresponding sequences in antibodiesderived from a particular species or belonging to a particular antibodyclass or subclass, while the remainder of the chain(s) is identical withor homologous to corresponding sequences in antibodies derived fromanother species or belonging to another antibody class or subclass, aswell as fragments of such antibodies, so long as they exhibit thedesired antagonistic activity (U.S. Pat. No. 4,816,567, which is herebyincorporated in its entirety).

Monoclonal antibodies of the invention may be prepared using hybridomamethods. In a hybridoma method, a mouse or other appropriate host animalis typically immunized with an immunizing agent to elicit lymphocytesthat produce or are capable of producing antibodies that willspecifically bind to the immunizing agent. Alternatively, thelymphocytes may be immunized in vitro.

The monoclonal antibodies may also be made by recombinant DNA methods,such as those described in U.S. Pat. No. 4,816,567. DNA encoding themonoclonal antibodies of the invention can be readily isolated andsequenced using conventional procedures (e.g., by using oligonucleotideprobes that are capable of binding specifically to genes encoding theheavy and light chains of murine antibodies).

In vitro methods are also suitable for preparing monovalent antibodies.Digestion of antibodies to produce fragments thereof, particularly Fabfragments, can be accomplished using routine techniques known in theart. For instance, digestion can be performed using papain. Examples ofpapain digestion are described in WO 94/29348 and U.S. Pat. No.4,342,566. Papain digestion of antibodies typically produces twoidentical antigen binding fragments, called Fab fragments, each with asingle antigen binding site, and a residual Fc fragment. Pepsintreatment yields a F(ab′)2 fragment and a pFc′ fragment.

The antibody fragments, whether attached to other sequences or not, canalso include insertions, deletions, substitutions, or other selectedmodifications of particular regions or specific amino acids residues,provided the activity of the fragment is not significantly altered orimpaired compared to the non-modified antibody or antibody fragment.These modifications can provide for some additional property, such as toremove/add amino acids capable of disulfide bonding, to increase itsbio-longevity, to alter its secretory characteristics, etc. In any case,the antibody fragment must possess a bioactive property, such as bindingactivity, regulation of binding at the binding domain, etc. Functionalor active regions of the antibody may be identified by mutagenesis of aspecific region of the protein, followed by expression and testing ofthe expressed polypeptide. Such methods are readily apparent to askilled practitioner in the art and can include site-specificmutagenesis of the nucleic acid encoding the antibody fragment.

The antibodies of the invention may further comprise humanizedantibodies or human antibodies. Humanized forms of non-human (e.g.,murine) antibodies are chimeric immunoglobulins, immunoglobulin chainsor fragments thereof (such as Fv, Fab, Fab′ or other antigen-bindingsubsequences of antibodies) which contain minimal sequence derived fromnon-human immunoglobulin. Humanized antibodies include humanimmunoglobulins (recipient antibody) in which residues from acomplementary determining region (CDR) of the recipient are replaced byresidues from a CDR of a non-human species (donor antibody) such asmouse, rat or rabbit having the desired specificity, affinity andcapacity. In some instances, Fv framework (FR) residues of the humanimmunoglobulin are replaced by corresponding non-human residues.Humanized antibodies may also comprise residues which are found neitherin the recipient antibody nor in the imported CDR or frameworksequences. In general, the humanized antibody will comprisesubstantially all of at least one, and typically two, variable domains,in which all or substantially all of the CDR regions correspond to thoseof a non-human immunoglobulin and all or substantially all of the FRregions are those of a human immunoglobulin consensus sequence. Thehumanized antibody optimally also will comprise at least a portion of animmunoglobulin constant region (Fc), typically that of a humanimmunoglobulin.

Methods for humanizing non-human antibodies are well known in the art.Generally, a humanized antibody has one or more amino acid residuesintroduced into it from a source which is non-human. These non-humanamino acid residues are often referred to as “import” residues, whichare typically taken from an “import” variable domain. Humanization canbe essentially performed by substituting rodent CDRs or CDR sequencesfor the corresponding sequences of a human antibody. Accordingly, such“humanized” antibodies are chimeric antibodies (U.S. Pat. No.4,816,567), wherein substantially less than an intact human variabledomain has been substituted by the corresponding sequence from anon-human species. In practice, humanized antibodies are typically humanantibodies in which some CDR residues and possibly some FR residues aresubstituted by residues from analogous sites in rodent antibodies.

Transgenic animals (e.g., mice) that are capable, upon immunization, ofproducing a full repertoire of human antibodies in the absence ofendogenous immunoglobulin production can be employed. For example, ithas been described that the homozygous deletion of the antibody heavychain joining region gene in chimeric and germ-line mutant mice resultsin complete inhibition of endogenous antibody production. Transfer ofthe human germ-line immunoglobulin gene array in such germ-line mutantmice will result in the production of human antibodies upon antigenchallenge. Human antibodies can also be produced in phage displaylibraries.

Antibodies of the invention are preferably administered to a subject ina pharmaceutically acceptable carrier. Typically, an appropriate amountof a pharmaceutically-acceptable salt is used in the formulation torender the formulation isotonic. Examples of thepharmaceutically-acceptable carrier include saline, Ringer's solutionand dextrose solution. The pH of the solution is preferably from about 5to about 8, and more preferably from about 7 to about 7.5. Furthercarriers include sustained release preparations such as semipermeablematrices of solid hydrophobic polymers containing the antibody, whichmatrices are in the form of shaped articles, e.g., films, liposomes ormicroparticles. It will be apparent to those persons skilled in the artthat certain carriers may be more preferable depending upon, forinstance, the route of administration and concentration of antibodybeing administered.

The antibodies can be administered to the subject, patient, or cell byinjection (e.g., intravenous, intraperitoneal, subcutaneous,intramuscular), or by other methods such as infusion that ensure itsdelivery to the bloodstream in an effective form. The antibodies mayalso be administered by intratumoral or peritumoral routes, to exertlocal as well as systemic therapeutic effects. Local or intravenousinjection is preferred.

Effective dosages and schedules for administering the antibodies may bedetermined empirically, and making such determinations is within theskill in the art. Those skilled in the art will understand that thedosage of antibodies that must be administered will vary depending on,for example, the subject that will receive the antibody, the route ofadministration, the particular type of antibody used and other drugsbeing administered. A typical daily dosage of the antibody used alonemight range from about 1 (μg/kg to up to 100 mg/kg of body weight ormore per day, depending on the factors mentioned above. Followingadministration of an antibody, preferably for treating ovarian cancer,the efficacy of the therapeutic antibody can be assessed in various wayswell known to the skilled practitioner. For instance, the size, number,and/or distribution of cancer in a subject receiving treatment may bemonitored using standard tumor imaging techniques. Atherapeutically-administered antibody that arrests tumor growth, resultsin tumor shrinkage, and/or prevents the development of new tumors,compared to the disease course that would occurs in the absence ofantibody administration, is an efficacious antibody for treatment ofcancer.

It is a further aspect of the invention to provide a method forproducing a soluble T-cell receptor (sTCR) recognizing a specificpeptide-MHC complex. Such soluble T-cell receptors can be generated fromspecific T-cell clones, and their affinity can be increased bymutagenesis targeting the complementarity-determining regions. For thepurpose of T-cell receptor selection, phage display can be used (US2010/0113300, (Liddy et al., 2012)). For the purpose of stabilization ofT-cell receptors during phage display and in case of practical use asdrug, alpha and beta chain can be linked e.g. by non-native disulfidebonds, other covalent bonds (single-chain T-cell receptor), or bydimerization domains (Boulter et al., 2003; Card et al., 2004; Willcoxet al., 1999). The T-cell receptor can be linked to toxins, drugs,cytokines (see, for example, US 2013/0115191), and domains recruitingeffector cells such as an anti-CD3 domain, etc., in order to executeparticular functions on target cells. Moreover, it could be expressed inT cells used for adoptive transfer. Further information can be found inWO 2004/033685A1 and WO 2004/074322A1. A combination of sTCRs isdescribed in WO 2012/056407A1. Further methods for the production aredisclosed in WO 2013/057586A1.

In addition, the peptides and/or the TCRs or antibodies or other bindingmolecules of the present invention can be used to verify a pathologist'sdiagnosis of a cancer based on a biopsied sample.

The antibodies or TCRs may also be used for in vivo diagnostic assays.Generally, the antibody is labeled with a radionucleotide (such as¹¹¹In, ⁹⁹Tc, ¹⁴C, ¹³¹I, ³H, ³²P or ³⁵S) so that the tumor can belocalized using immunoscintiography. In one embodiment, antibodies orfragments thereof bind to the extracellular domains of two or moretargets of a protein selected from the group consisting of theabove-mentioned proteins, and the affinity value (Kd) is less than 1×10μM.

Antibodies for diagnostic use may be labeled with probes suitable fordetection by various imaging methods. Methods for detection of probesinclude, but are not limited to, fluorescence, light, confocal andelectron microscopy; magnetic resonance imaging and spectroscopy;fluoroscopy, computed tomography and positron emission tomography.Suitable probes include, but are not limited to, fluorescein, rhodamine,eosin and other fluorophores, radioisotopes, gold, gadolinium and otherlanthanides, paramagnetic iron, fluorine-18 and other positron-emittingradionuclides. Additionally, probes may be bi- or multi-functional andbe detectable by more than one of the methods listed. These antibodiesmay be directly or indirectly labeled with said probes. Attachment ofprobes to the antibodies includes covalent attachment of the probe,incorporation of the probe into the antibody, and the covalentattachment of a chelating compound for binding of probe, amongst otherswell recognized in the art. For immunohistochemistry, the disease tissuesample may be fresh or frozen or may be embedded in paraffin and fixedwith a preservative such as formalin. The fixed or embedded sectioncontains the sample are contacted with a labeled primary antibody andsecondary antibody, wherein the antibody is used to detect theexpression of the proteins in situ.

Another aspect of the present invention includes an in vitro method forproducing activated T cells, the method comprising contacting in vitro Tcells with antigen loaded human MHC molecules expressed on the surfaceof a suitable antigen-presenting cell for a period of time sufficient toactivate the T cell in an antigen specific manner, wherein the antigenis a peptide according to the invention. Preferably a sufficient amountof the antigen is used with an antigen-presenting cell.

Preferably the mammalian cell lacks or has a reduced level or functionof the TAP peptide transporter. Suitable cells that lack the TAP peptidetransporter include T2, RMA-S and Drosophila cells. TAP is thetransporter associated with antigen processing.

The human peptide loading deficient cell line T2 is available from theAmerican Type Culture Collection, 12301 Parklawn Drive, Rockville, Md.20852, USA under Catalogue No CRL 1992; the Drosophila cell lineSchneider line 2 is available from the ATCC under Catalogue No CRL19863; the mouse RMA-S cell line is described in Ljunggren et al.(Ljunggren and Karre, 1985).

Preferably, before transfection the host cell expresses substantially noMHC class I molecules. It is also preferred that the stimulator cellexpresses a molecule important for providing a co-stimulatory signal forT-cells such as any of B7.1, B7.2, ICAM-1 and LFA 3. The nucleic acidsequences of numerous MHC class I molecules and of the co-stimulatormolecules are publicly available from the GenBank and EMBL databases.

In case of a MHC class I epitope being used as an antigen, the T cellsare CD8-positive T cells.

If an antigen-presenting cell is transfected to express such an epitope,preferably the cell comprises an expression vector capable of expressinga peptide containing SEQ ID NO: 1 to SEQ ID NO: 772, or a variant aminoacid sequence thereof.

A number of other methods may be used for generating T cells in vitro.For example, autologous tumor-infiltrating lymphocytes can be used inthe generation of CTL. Plebanski et al. (Plebanski et al., 1995) madeuse of autologous peripheral blood lymphocytes (PLBs) in the preparationof T cells. Furthermore, the production of autologous T cells by pulsingdendritic cells with peptide or polypeptide, or via infection withrecombinant virus is possible. Also, B cells can be used in theproduction of autologous T cells. In addition, macrophages pulsed withpeptide or polypeptide, or infected with recombinant virus, may be usedin the preparation of autologous T cells. S. Walter et al. (Walter etal., 2003) describe the in vitro priming of T cells by using artificialantigen presenting cells (aAPCs), which is also a suitable way forgenerating T cells against the peptide of choice. In the presentinvention, aAPCs were generated by the coupling of preformed MHC:peptidecomplexes to the surface of polystyrene particles (microbeads) bybiotin:streptavidin biochemistry. This system permits the exact controlof the MHC density on aAPCs, which allows to selectively eliciting high-or low-avidity antigen-specific T cell responses with high efficiencyfrom blood samples. Apart from MHC:peptide complexes, aAPCs should carryother proteins with co-stimulatory activity like anti-CD28 antibodiescoupled to their surface. Furthermore such aAPC-based systems oftenrequire the addition of appropriate soluble factors, e. g. cytokines,like interleukin-12.

Allogeneic cells may also be used in the preparation of T cells and amethod is described in detail in WO 97/26328, incorporated herein byreference. For example, in addition to Drosophila cells and T2 cells,other cells may be used to present antigens such as CHO cells,baculovirus-infected insect cells, bacteria, yeast, andvaccinia-infected target cells. In addition plant viruses may be used(see, for example, Porta et al. (Porta et al., 1994) which describes thedevelopment of cowpea mosaic virus as a high-yielding system for thepresentation of foreign peptides.

The activated T cells that are directed against the peptides of theinvention are useful in therapy. Thus, a further aspect of the inventionprovides activated T cells obtainable by the foregoing methods of theinvention.

Activated T cells, which are produced by the above method, willselectively recognize a cell that aberrantly expresses a polypeptidethat comprises an amino acid sequence of SEQ ID NO: 1 to SEQ ID NO 772.

Preferably, the T cell recognizes the cell by interacting through itsTCR with the HLA/peptide-complex (for example, binding). The T cells areuseful in a method of killing target cells in a patient whose targetcells aberrantly express a polypeptide comprising an amino acid sequenceof the invention wherein the patient is administered an effective numberof the activated T cells. The T cells that are administered to thepatient may be derived from the patient and activated as described above(i.e. they are autologous T cells). Alternatively, the T cells are notfrom the patient but are from another individual. Of course, it ispreferred if the individual is a healthy individual. By “healthyindividual” the inventors mean that the individual is generally in goodhealth, preferably has a competent immune system and, more preferably,is not suffering from any disease that can be readily tested for, anddetected.

In vivo, the target cells for the CD8-positive T cells according to thepresent invention can be cells of the tumor (which sometimes express MHCclass II) and/or stromal cells surrounding the tumor (tumor cells)(which sometimes also express MHC class II; (Dengjel et al., 2006)).

The T cells of the present invention may be used as active ingredientsof a therapeutic composition. Thus, the invention also provides a methodof killing target cells in a patient whose target cells aberrantlyexpress a polypeptide comprising an amino acid sequence of theinvention, the method comprising administering to the patient aneffective number of T cells as defined above.

By “aberrantly expressed” the inventors also mean that the polypeptideis over-expressed compared to levels of expression in normal tissues orthat the gene is silent in the tissue from which the tumor is derivedbut in the tumor it is expressed. By “over-expressed” the inventors meanthat the polypeptide is present at a level at least 1.2-fold of thatpresent in normal tissue; preferably at least 2-fold, and morepreferably at least 5-fold or 10-fold the level present in normaltissue.

T cells may be obtained by methods known in the art, e.g. thosedescribed above.

Protocols for this so-called adoptive transfer of T cells are well knownin the art. Reviews can be found in: Gattioni et al. and Morgan et al.(Gattinoni et al., 2006; Morgan et al., 2006).

Another aspect of the present invention includes the use of the peptidescomplexed with MHC to generate a T-cell receptor whose nucleic acid iscloned and is introduced into a host cell, preferably a T cell. Thisengineered T cell can then be transferred to a patient for therapy ofcancer.

Any molecule of the invention, i.e. the peptide, nucleic acid, antibody,expression vector, cell, activated T cell, T-cell receptor or thenucleic acid encoding it, is useful for the treatment of disorders,characterized by cells escaping an immune response. Therefore anymolecule of the present invention may be used as medicament or in themanufacture of a medicament. The molecule may be used by itself orcombined with other molecule(s) of the invention or (a) knownmolecule(s).

The present invention is further directed at a kit comprising:

(a) a container containing a pharmaceutical composition as describedabove, in solution or in lyophilized form;

(b) optionally a second container containing a diluent or reconstitutingsolution for the lyophilized formulation; and

(c) optionally, instructions for (i) use of the solution or (ii)reconstitution and/or use of the lyophilized formulation.

The kit may further comprise one or more of (iii) a buffer, (iv) adiluent, (v) a filter, (vi) a needle, or (v) a syringe. The container ispreferably a bottle, a vial, a syringe or test tube; and it may be amulti-use container. The pharmaceutical composition is preferablylyophilized.

Kits of the present invention preferably comprise a lyophilizedformulation of the present invention in a suitable container andinstructions for its reconstitution and/or use. Suitable containersinclude, for example, bottles, vials (e.g. dual chamber vials), syringes(such as dual chamber syringes) and test tubes. The container may beformed from a variety of materials such as glass or plastic. Preferablythe kit and/or container contain/s instructions on or associated withthe container that indicates directions for reconstitution and/or use.For example, the label may indicate that the lyophilized formulation isto be reconstituted to peptide concentrations as described above. Thelabel may further indicate that the formulation is useful or intendedfor subcutaneous administration.

The container holding the formulation may be a multi-use vial, whichallows for repeat administrations (e.g., from 2-6 administrations) ofthe reconstituted formulation. The kit may further comprise a secondcontainer comprising a suitable diluent (e.g., sodium bicarbonatesolution).

Upon mixing of the diluent and the lyophilized formulation, the finalpeptide concentration in the reconstituted formulation is preferably atleast 0.15 mg/mL/peptide (=75 μg) and preferably not more than 3mg/mL/peptide (=1500 μg). The kit may further include other materialsdesirable from a commercial and user standpoint, including otherbuffers, diluents, filters, needles, syringes, and package inserts withinstructions for use.

Kits of the present invention may have a single container that containsthe formulation of the pharmaceutical compositions according to thepresent invention with or without other components (e.g., othercompounds or pharmaceutical compositions of these other compounds) ormay have distinct container for each component.

Preferably, kits of the invention include a formulation of the inventionpackaged for use in combination with the co-administration of a secondcompound (such as adjuvants (e.g. GM-CSF), a chemotherapeutic agent, anatural product, a hormone or antagonist, an anti-angiogenesis agent orinhibitor, an apoptosis-inducing agent or a chelator) or apharmaceutical composition thereof. The components of the kit may bepre-complexed or each component may be in a separate distinct containerprior to administration to a patient. The components of the kit may beprovided in one or more liquid solutions, preferably, an aqueoussolution, more preferably, a sterile aqueous solution. The components ofthe kit may also be provided as solids, which may be converted intoliquids by addition of suitable solvents, which are preferably providedin another distinct container.

The container of a therapeutic kit may be a vial, test tube, flask,bottle, syringe, or any other means of enclosing a solid or liquid.Usually, when there is more than one component, the kit will contain asecond vial or other container, which allows for separate dosing. Thekit may also contain another container for a pharmaceutically acceptableliquid. Preferably, a therapeutic kit will contain an apparatus (e.g.,one or more needles, syringes, eye droppers, pipette, etc.), whichenables administration of the agents of the invention that arecomponents of the present kit.

The present formulation is one that is suitable for administration ofthe peptides by any acceptable route such as oral (enteral), nasal,ophthal, subcutaneous, intradermal, intramuscular, intravenous ortransdermal. Preferably, the administration is s.c., and most preferablyi.d. administration may be by infusion pump.

Since the peptides of the invention were isolated from ovarian cancer,the medicament of the invention is preferably used to treat ovariancancer.

The present invention further relates to a method for producing apersonalized pharmaceutical for an individual patient comprisingmanufacturing a pharmaceutical composition comprising at least onepeptide selected from a warehouse of pre-screened TUMAPs, wherein the atleast one peptide used in the pharmaceutical composition is selected forsuitability in the individual patient. In one embodiment, thepharmaceutical composition is a vaccine. The method could also beadapted to produce T cell clones for down-stream applications, such asTCR isolations, or soluble antibodies, and other treatment options.

A “personalized pharmaceutical” shall mean specifically tailoredtherapies for one individual patient that will only be used for therapyin such individual patient, including actively personalized cancervaccines and adoptive cellular therapies using autologous patienttissue.

As used herein, the term “warehouse” shall refer to a group or set ofpeptides that have been pre-screened for immunogenicity and/orover-presentation in a particular tumor type. The term “warehouse” isnot intended to imply that the particular peptides included in thevaccine have been pre-manufactured and stored in a physical facility,although that possibility is contemplated. It is expressly contemplatedthat the peptides may be manufactured de novo for each individualizedvaccine produced, or may be pre-manufactured and stored. The warehouse(e.g. in the form of a database) is composed of tumor-associatedpeptides which were highly overexpressed in the tumor tissue of ovariancancer patients with various HLA-A HLA-B and HLA-C alleles. It maycontain MHC class I and MHC class II peptides or elongated MHC class Ipeptides. In addition to the tumor associated peptides collected fromseveral ovarian cancer tissues, the warehouse may contain HLA-A*02,HLA-A*01, HLA-A*03, HLA-A*24, HLA-B*07, HLA-B*08 and HLA-B*44 markerpeptides. These peptides allow comparison of the magnitude of T-cellimmunity induced by TUMAPS in a quantitative manner and hence allowimportant conclusion to be drawn on the capacity of the vaccine toelicit anti-tumor responses. Secondly, they function as importantpositive control peptides derived from a “non-self” antigen in the casethat any vaccine-induced T-cell responses to TUMAPs derived from “self”antigens in a patient are not observed. And thirdly, it may allowconclusions to be drawn, regarding the status of immunocompetence of thepatient.

TUMAPs for the warehouse are identified by using an integratedfunctional genomics approach combining gene expression analysis, massspectrometry, and T-cell immunology (XPresident®). The approach assuresthat only TUMAPs truly present on a high percentage of tumors but not oronly minimally expressed on normal tissue, are chosen for furtheranalysis. For initial peptide selection, ovarian cancer samples frompatients and blood from healthy donors were analyzed in a stepwiseapproach:

1. HLA ligands from the malignant material were identified by massspectrometry

2. Genome-wide messenger ribonucleic acid (mRNA) expression analysis wasused to identify genes over-expressed in the malignant tissue (ovariancancer) compared with a range of normal organs and tissues

3. Identified HLA ligands were compared to gene expression data.Peptides presented on tumor tissue, preferably encoded by selectivelyexpressed or over-expressed genes as detected in step 2 were consideredsuitable TUMAP candidates for a multi-peptide vaccine.4. Literature research was performed in order to identify additionalevidence supporting the relevance of the identified peptides as TUMAPs5. The relevance of over-expression at the mRNA level was confirmed byredetection of selected TUMAPs from step 3 on tumor tissue and lack of(or infrequent) detection on healthy tissues.6. In order to assess, whether an induction of in vivo T-cell responsesby the selected peptides may be feasible, in vitro immunogenicity assayswere performed using human T cells from healthy donors as well as fromovarian cancer patients.

In an aspect, the peptides are pre-screened for immunogenicity beforebeing included in the warehouse. By way of example, and not limitation,the immunogenicity of the peptides included in the warehouse isdetermined by a method comprising in vitro T-cell priming throughrepeated stimulations of CD8+ T cells from healthy donors withartificial antigen presenting cells loaded with peptide/MHC complexesand anti-CD28 antibody.

This method is preferred for rare cancers and patients with a rareexpression profile. In contrast to multi-peptide cocktails with a fixedcomposition as currently developed, the warehouse allows a significantlyhigher matching of the actual expression of antigens in the tumor withthe vaccine. Selected single or combinations of several “off-the-shelf”peptides will be used for each patient in a multitarget approach. Intheory, an approach based on selection of e.g. 5 different antigenicpeptides from a library of 50 would already lead to approximately 17million possible drug product (DP) compositions.

In an aspect, the peptides are selected for inclusion in the vaccinebased on their suitability for the individual patient based on themethod according to the present invention as described herein, or asbelow.

The HLA phenotype, transcriptomic and peptidomic data is gathered fromthe patient's tumor material, and blood samples to identify the mostsuitable peptides for each patient containing “warehouse” andpatient-unique (i.e. mutated) TUMAPs. Those peptides will be chosen,which are selectively or over-expressed in the patients' tumor and,where possible, show strong in vitro immunogenicity if tested with thepatients' individual PBMCs.

Preferably, the peptides included in the vaccine are identified by amethod comprising: (a) identifying tumor-associated peptides (TUMAPs)presented by a tumor sample from the individual patient; (b) comparingthe peptides identified in (a) with a warehouse (database) of peptidesas described above; and (c) selecting at least one peptide from thewarehouse (database) that correlates with a tumor-associated peptideidentified in the patient. For example, the TUMAPs presented by thetumor sample are identified by: (a1) comparing expression data from thetumor sample to expression data from a sample of normal tissuecorresponding to the tissue type of the tumor sample to identifyproteins that are over-expressed or aberrantly expressed in the tumorsample; and (a2) correlating the expression data with sequences of MHCligands bound to MHC class I and/or class II molecules in the tumorsample to identify MHC ligands derived from proteins over-expressed oraberrantly expressed by the tumor. Preferably, the sequences of MHCligands are identified by eluting bound peptides from MHC moleculesisolated from the tumor sample, and sequencing the eluted ligands.Preferably, the tumor sample and the normal tissue are obtained from thesame patient.

In addition to, or as an alternative to, selecting peptides using awarehousing (database) model, TUMAPs may be identified in the patient denovo, and then included in the vaccine. As one example, candidate TUMAPsmay be identified in the patient by (a1) comparing expression data fromthe tumor sample to expression data from a sample of normal tissuecorresponding to the tissue type of the tumor sample to identifyproteins that are over-expressed or aberrantly expressed in the tumorsample; and (a2) correlating the expression data with sequences of MHCligands bound to MHC class I and/or class II molecules in the tumorsample to identify MHC ligands derived from proteins over-expressed oraberrantly expressed by the tumor. As another example, proteins may beidentified containing mutations that are unique to the tumor samplerelative to normal corresponding tissue from the individual patient, andTUMAPs can be identified that specifically target the mutation. Forexample, the genome of the tumor and of corresponding normal tissue canbe sequenced by whole genome sequencing: For discovery of non-synonymousmutations in the protein-coding regions of genes, genomic DNA and RNAare extracted from tumor tissues and normal non-mutated genomic germlineDNA is extracted from peripheral blood mononuclear cells (PBMCs). Theapplied NGS approach is confined to the re-sequencing of protein codingregions (exome re-sequencing). For this purpose, exonic DNA from humansamples is captured using vendor-supplied target enrichment kits,followed by sequencing with e.g. a HiSeq2000 (Illumina). Additionally,tumor mRNA is sequenced for direct quantification of gene expression andvalidation that mutated genes are expressed in the patients' tumors. Theresultant millions of sequence reads are processed through softwarealgorithms. The output list contains mutations and gene expression.Tumor-specific somatic mutations are determined by comparison with thePBMC-derived germline variations and prioritized. The de novo identifiedpeptides can then be tested for immunogenicity as described above forthe warehouse, and candidate TUMAPs possessing suitable immunogenicityare selected for inclusion in the vaccine.

In one exemplary embodiment, the peptides included in the vaccine areidentified by: (a) identifying tumor-associated peptides (TUMAPs)presented by a tumor sample from the individual patient by the method asdescribed above; (b) comparing the peptides identified in a) with awarehouse of peptides that have been prescreened for immunogenicity andoverpresentation in tumors as compared to corresponding normal tissue;(c) selecting at least one peptide from the warehouse that correlateswith a tumor-associated peptide identified in the patient; and (d)optionally, selecting at least one peptide identified de novo in (a)confirming its immunogenicity.

In one exemplary embodiment, the peptides included in the vaccine areidentified by: (a) identifying tumor-associated peptides (TUMAPs)presented by a tumor sample from the individual patient; and (b)selecting at least one peptide identified de novo in (a) and confirmingits immunogenicity.

Once the peptides for a personalized peptide based vaccine are selected,the vaccine is produced. The vaccine preferably is a liquid formulationconsisting of the individual peptides dissolved in between 20-40% DMSO,preferably about 30-35% DMSO, such as about 33% DMSO.

Each peptide to be included into a product is dissolved in DMSO. Theconcentration of the single peptide solutions has to be chosen dependingon the number of peptides to be included into the product. The singlepeptide-DMSO solutions are mixed in equal parts to achieve a solutioncontaining all peptides to be included in the product with aconcentration of ˜2.5 mg/ml per peptide. The mixed solution is thendiluted 1:3 with water for injection to achieve a concentration of 0.826mg/ml per peptide in 33% DMSO. The diluted solution is filtered througha 0.22 μm sterile filter. The final bulk solution is obtained.

Final bulk solution is filled into vials and stored at −20° C. untiluse. One vial contains 700 μL solution, containing 0.578 mg of eachpeptide. Of this, 500 μL (approx. 400 pg per peptide) will be appliedfor intradermal injection.

In addition to being useful for treating cancer, the peptides of thepresent invention are also useful as diagnostics. Since the peptideswere generated from ovarian cancer cells and since it was determinedthat these peptides are not or at lower levels present in normaltissues, these peptides can be used to diagnose the presence of acancer.

The presence of claimed peptides on tissue biopsies in blood samples canassist a pathologist in diagnosis of cancer. Detection of certainpeptides by means of antibodies, mass spectrometry or other methodsknown in the art can tell the pathologist that the tissue sample ismalignant or inflamed or generally diseased, or can be used as abiomarker for ovarian cancer. Presence of groups of peptides can enableclassification or sub-classification of diseased tissues.

The detection of peptides on diseased tissue specimen can enable thedecision about the benefit of therapies involving the immune system,especially if T-lymphocytes are known or expected to be involved in themechanism of action. Loss of MHC expression is a well describedmechanism by which infected of malignant cells escapeimmuno-surveillance. Thus, presence of peptides shows that thismechanism is not exploited by the analyzed cells.

The peptides of the present invention might be used to analyzelymphocyte responses against those peptides such as T cell responses orantibody responses against the peptide or the peptide complexed to MHCmolecules. These lymphocyte responses can be used as prognostic markersfor decision on further therapy steps. These responses can also be usedas surrogate response markers in immunotherapy approaches aiming toinduce lymphocyte responses by different means, e.g. vaccination ofprotein, nucleic acids, autologous materials, adoptive transfer oflymphocytes. In gene therapy settings, lymphocyte responses againstpeptides can be considered in the assessment of side effects. Monitoringof lymphocyte responses might also be a valuable tool for follow-upexaminations of transplantation therapies, e.g. for the detection ofgraft versus host and host versus graft diseases.

The present invention will now be described in the following exampleswhich describe preferred embodiments thereof, and with reference to theaccompanying figures, nevertheless, without being limited thereto. Forthe purposes of the present invention, all references as cited hereinare incorporated by reference in their entireties.

FIGURES

FIGS. 1A through 1S show exemplary expression profile of source genes ofthe present invention that are over-expressed in different cancersamples. Tumor (black dots) and normal (grey dots) samples are groupedaccording to organ of origin, and box-and-whisker plots representmedian, 25th and 75th percentile (box), and minimum and maximum(whiskers) RPKM values. Normal organs are ordered according to riskcategories. RPKM=reads per kilobase per million mapped reads. Normalsamples: blood cells; blood vessel; brain; heart; liver; lung; adipose:adipose tissue; adren.gl.: adrenal gland; bile duct; bladder; BM: bonemarrow; cartilage; esoph: esophagus; eye; gallb: gallbladder; head andneck; kidney; large_int: large intestine; LN: lymph node; nerve;pancreas; parathyr: parathyroid; pituit: pituitary; skel.mus: skeletalmuscle; skin; small_int: small intestine; spleen; stomach; thyroid;trachea; bladder; breast; ovary; placenta; prostate; testis; thymus;uterus. Tumor samples: AML: acute myeloid leukemia; BRCA: breast cancer;CLL: chronic lymphocytic leukemia; CRC: colorectal cancer; GALB:gallbladder cancer; GB: glioblastoma; GC: gastric cancer; HCC:hepatocellular carcinoma; HNSCC: head-and-neck cancer; MEL: melanoma;NHL: non-hodgkin lymphoma; NSCLC: non-small cell lung cancer; OC:ovarian cancer; OSC_GC: esophageal/gastric cancer; OSCAR: esophagealcancer; PC: pancreatic cancer; PCA: prostate cancer; RCC: renal cellcarcinoma; SCLC: small cell lung cancer; UBC: urinary bladder carcinoma;UEC: uterine and endometrial cancer. FIG. 1A) Gene symbol: CT45A2,Peptide: KYEKIFEML (SEQ ID No.: 12), FIG. 1B) Gene symbol: NLRP2,Peptide: VLYGPAGLGK (SEQ ID No.: 27), FIG. 1C) Gene symbol: NLRP7,Peptide: LLDEGAMLLY (SEQ ID No.: 31), FIG. 1D) Gene symbol: HTR3A,Peptide: GLLQELSSI (SEQ ID No.: 66), FIG. 1E) Gene symbol: VTCN1,Peptide: KVVSVLYNV (SEQ ID No.: 75), FIG. 1F) Gene symbol: CYP2W1,Peptide: RYGPVFTV (SEQ ID No.: 98), FIG. 1G) Gene symbol: MMP11,Peptide: LLQPPPLLAR (SEQ ID No.: 98), FIG. 1H) Gene symbol: MMP12,Peptide: FVDNQYWRY (SEQ ID No.: 115), FIG. 1I) Gene symbol: CTAG2,Peptide: APLPRPGAVL (SEQ ID No.: 119), FIG. 1J) Gene symbol: FAM111B,Peptide: KPSESIYSAL (SEQ ID No.: 123), FIG. 1K) Gene symbol: CCNA1,Peptide: HLLLKVLAF (SEQ ID No.: 151), FIG. 1L) Gene symbol: FAM83H,Peptide: HVKEKFLL (SEQ ID No.: 156), FIG. 1M) Gene symbol: MAGEA11,Peptide: KEVDPTSHSY (SEQ ID No.: 194), FIG. 1N) Gene symbol: MMP11,Peptide: YTFRYPLSL (SEQ ID No.: 227), FIG. 1O) Gene symbol: ZNF560,Peptide: VFVSFSSLF (SEQ ID No.: 255), FIG. 1P) Gene symbol: IGF2BP1,Peptide: ISYSGQFLVK (SEQ ID No.: 266), FIG. 1Q) Gene symbol: CLDN6,Peptide: LPMWKVTAF (SEQ ID No.: 303), FIG. 1R) Gene symbol: IGF2BP3,Peptide: IEALSGKIEL (SEQ ID No.: 413), FIG. 1S) Gene symbol: PRAME,Peptide: EEQYIAQF (SEQ ID No.: 432).

FIGS. 1T through 1V show exemplary expression profiles of source genesof the present invention, that are over-expressed in different cancersamples. Tumor (black dots) and normal (grey dots) samples are groupedaccording to organ of origin. Box-and-whisker plots represent medianFPKM value, 25th and 75th percentile (box) plus whiskers that extend tothe lowest data point still within 1.5 interquartile range (IQR) of thelower quartile and the highest data point still within 1.5 IQR of theupper quartile. Normal organs are ordered according to risk categories.FPKM: fragments per kilobase per million mapped reads. Normal samples:blood cells; bloodvess (blood vessels); brain; heart; liver; lung;adipose (adipose tissue); adrenal gl (adrenal gland); bile duct;bladder; bone marrow; cartilage; esoph (esophagus); eye; gall bl(gallbladder); head&neck; intest. la (large intestine); intest. sm(small intestine); kidney; lymph node; nerve perith (peripheral nerve);pancreas; parathyr (parathyroid gland); perit (peritoneum); pituit(pituitary); pleura; skel. mus (skeletal muscle); skin; spleen; stomach;thyroid; trachea; ureter; breast; ovary; placenta; prostate; testis;thymus; uterus. Tumor samples: AML (acute myeloid leukemia); BRCA(breast cancer); CCC (cholangiocellular carcinoma); CLL (chroniclymphocytic leukemia); CRC (colorectal cancer); GBC (gallbladdercancer); GBM (glioblastoma); GC (gastric cancer); HCC (hepatocellularcarcinoma); HNSCC (head and neck squamous cell carcinoma); MEL(melanoma); NHL (non-hodgkin lymphoma); NSCLCadeno (non-small cell lungcancer adenocarcinoma); NSCLCother (NSCLC samples that could notunambiguously be assigned to NSCLCadeno or NSCLCsquam); NSCLCsquam(squamous cell non-small cell lung cancer); OC (ovarian cancer); OSCAR(esophageal cancer); PACA (pancreatic cancer); PRCA (prostate cancer);RCC (renal cell carcinoma); SCLC (small cell lung cancer); UBC (urinarybladder carcinoma); UEC (uterine and endometrial cancer). FIG. 1T) Genesymbol: MAGEA4, Peptide: SPDAESLFREALSNKVDEL (SEQ ID No.: 597), FIG. 1U)Gene symbol: MAGEA4, Peptide: LSNKVDELAHFLLRK (SEQ ID No.: 601), FIG.1V) Gene symbol: MAGEB3, Peptide: KLITQDLVKLKYLEYRQ (SEQ ID No.: 604).

FIG. 2 shows exemplary results of peptide-specific in vitro CD8+ T cellresponses of a healthy HLA-A*02+ donor. CD8+ T cells were primed usingartificial APCs coated with anti-CD28 mAb and HLA-A*02 in complex withSeqID No 773 peptide (ALYGKLLKL, Seq ID NO: 773) left panel. After threecycles of stimulation, the detection of peptide-reactive cells wasperformed by 2D multimer staining with A*02/SeqID No 773. Right panelshows control staining of cells stimulated with irrelevant A*02/peptidecomplexes. Viable singlet cells were gated for CD8+ lymphocytes. Booleangates helped excluding false-positive events detected with multimersspecific for different peptides. Frequencies of specific multimer+ cellsamong CD8+ lymphocytes are indicated.

FIG. 3 shows exemplary results of peptide-specific in vitro CD8+ T cellresponses of a healthy HLA-A*24+ donor. CD8+ T cells were primed usingartificial APCs coated with anti-CD28 mAb and HLA-A*24 in complex withSeqID No 774 peptide (left panel). After three cycles of stimulation,the detection of peptide-reactive cells was performed by 2D multimerstaining with A*24/SeqID No 774 (VYVDDIYVI, Seq ID NO: 774). Right panelshows control staining of cells stimulated with irrelevant A*24/peptidecomplexes. Viable singlet cells were gated for CD8+ lymphocytes. Booleangates helped excluding false-positive events detected with multimersspecific for different peptides. Frequencies of specific multimer+ cellsamong CD8+ lymphocytes are indicated.

FIGS. 4A and 4B shows exemplary results of peptide-specific in vitroCD8+ T cell responses of a healthy HLA-A*02+ donor. CD8+ T cells wereprimed using artificial APCs coated with anti-CD28 mAb and HLA-A*02 incomplex with SeqID No 67 peptide SLLLPSIFL (FIG. 4A, left panel) andSeqID No 75 peptide KVVSVLYNV (FIG. 4B, left panel), respectively. Afterthree cycles of stimulation, the detection of peptide-reactive cells wasperformed by 2D multimer staining with A*02/SeqID No 67 (FIG. 4A) orA*02/SeqID No 75 (FIG. 4B). Right panels (FIGS. 4A and 4B) show controlstaining of cells stimulated with irrelevant A*02/peptide complexes.Viable singlet cells were gated for CD8+ lymphocytes. Boolean gateshelped excluding false-positive events detected with multimers specificfor different peptides. Frequencies of specific multimer+ cells amongCD8+ lymphocytes are indicated.

FIGS. 5A and 5B shows exemplary results of peptide-specific in vitroCD8+ T cell responses of a healthy HLA-A*24+ donor. CD8+ T cells wereprimed using artificial APCs coated with anti-CD28 mAb and HLA-A*24 incomplex with SeqID No 11 peptide SYSDLHYGF (FIG. 5A, left panel) andSeqID No 79 peptide SYNEHWNYL (FIG. 5B, left panel), respectively. Afterthree cycles of stimulation, the detection of peptide-reactive cells wasperformed by 2D multimer staining with A*24/SeqID No 11 (FIG. 5A) orA*24/SeqID No 79 (FIG. 5B). Right panels (FIGS. 5A and 5B) show controlstaining of cells stimulated with irrelevant A*24/peptide complexes.Viable singlet cells were gated for CD8+ lymphocytes. Boolean gateshelped excluding false-positive events detected with multimers specificfor different peptides. Frequencies of specific multimer+ cells amongCD8+ lymphocytes are indicated.

FIGS. 6A and 6B show exemplary results of peptide-specific in vitro CD8+T cell responses of a healthy HLA-B*07+ donor. CD8+ T cells were primedusing artificial APCs coated with anti-CD28 mAb and HLA-B*07 in complexwith SeqID No 33 peptide SPTFHLTL (FIG. 6A, left panel) and SeqID No 40peptide KPGTSYRVTL (FIG. 6B, left panel), respectively. After threecycles of stimulation, the detection of peptide-reactive cells wasperformed by 2D multimer staining with B*07/SeqID No 33 (FIG. 6A) orB*07/SeqID No 40 (FIG. 6B). Right panels (FIGS. 6A and 6B) show controlstaining of cells stimulated with irrelevant B*07/peptide complexes.Viable singlet cells were gated for CD8+ lymphocytes. Boolean gateshelped excluding false-positive events detected with multimers specificfor different peptides. Frequencies of specific multimer+ cells amongCD8+ lymphocytes are indicated.

FIGS. 7A and 7B shows exemplary results of peptide-specific in vitroCD8+ T cell responses of a healthy HLA-A*01+ donor. CD8+ T cells wereprimed using artificial APCs coated with anti-CD28 mAb and HLA-A*01 incomplex with SeqID No 113 peptide QLDSNRLTY (FIG. 7A, left panel) andSeqID No 115 peptide FVDNQYWRY (FIG. 7B, left panel), respectively.After three cycles of stimulation, the detection of peptide-reactivecells was performed by 2D multimer staining with A*01/SeqID No 113 (FIG.7A) or A*01/SeqID No 115 (FIG. 7B). Right panels (FIGS. 7A and 7B) showcontrol staining of cells stimulated with irrelevant A*01/peptidecomplexes. Viable singlet cells were gated for CD8+ lymphocytes. Booleangates helped excluding false-positive events detected with multimersspecific for different peptides. Frequencies of specific multimer+ cellsamong CD8+ lymphocytes are indicated.

FIGS. 8A and 8B shows exemplary results of peptide-specific in vitroCD8+ T cell responses of a healthy HLA-A*03+ donor. CD8+ T cells wereprimed using artificial APCs coated with anti-CD28 mAb and HLA-A*03 incomplex with SeqID No 23 peptide GMMKGGIRK (FIG. 8A, left panel) andSeqID No 90 peptide KVAGERYVYK (FIG. 8B, left panel), respectively.After three cycles of stimulation, the detection of peptide-reactivecells was performed by 2D multimer staining with A*03/SeqID No 23 (FIG.8A) or A*03/SeqID No 90 (FIG. 8B). Right panels (FIGS. 8A and 8B) showcontrol staining of cells stimulated with irrelevant A*03/peptidecomplexes. Viable singlet cells were gated for CD8+ lymphocytes. Booleangates helped excluding false-positive events detected with multimersspecific for different peptides. Frequencies of specific multimer+ cellsamong CD8+ lymphocytes are indicated.

FIGS. 9A and 9B shows exemplary results of peptide-specific in vitroCD8+ T cell responses of a healthy HLA-B*44+ donor. CD8+ T cells wereprimed using artificial APCs coated with anti-CD28 mAb and HLA-B*44 incomplex with SeqID No 200 peptide AESIPTVSF (FIG. 9A, left panel) andSeqID No 211 peptide EEKVFPSPLW (FIG. 9B, left panel), respectively.After three cycles of stimulation, the detection of peptide-reactivecells was performed by 2D multimer staining with B*44/SeqID No 200 (FIG.9A) or B*44/SeqID No 211 (FIG. 9B). Right panels (FIGS. 9A and 9B) showcontrol staining of cells stimulated with irrelevant B*44/peptidecomplexes. Viable singlet cells were gated for CD8+ lymphocytes. Booleangates helped excluding false-positive events detected with multimersspecific for different peptides. Frequencies of specific multimer+ cellsamong CD8+ lymphocytes are indicated.

EXAMPLES Example 1

Identification of Tumor Associated Peptides Presented on the CellSurface

Tissue Samples

Patients' tumor tissues and normal tissues were obtained from theUniversity Hospital Tübingen (Tübingen, Germany). Written informedconsents of all patients had been given before surgery or autopsy.Tissues were shock-frozen immediately after excision and stored untilisolation of TUMAPs at −70° C. or below.

Isolation of HLA Peptides from Tissue Samples

HLA peptide pools from shock-frozen tissue samples were obtained byimmune precipitation from solid tissues according to a slightly modifiedprotocol (Falk et al., 1991; Seeger et al., 1999) using theHLA-A*02-specific antibody BB7.2, the HLA-A, —B, C-specific antibodyW6/32, the HLA-DR specific antibody L243 and the pan-HLA class IIspecific antibody Tü39, CNBr-activated sepharose, acid treatment, andultrafiltration.

Mass Spectrometry Analyses

The HLA peptide pools as obtained were separated according to theirhydrophobicity by reversed-phase chromatography (Ultimate 3000 RSLC NanoUHPLC System, Dionex)) and the eluting peptides were analyzed inLTQ-Orbitrap and Fusion Lumos hybrid mass spectrometers (ThermoElectron)equipped with an ESI source. Peptide samples were loaded with 3% ofsolvent B (20% H₂O, 80% acetonitrile and 0.04% formic acid) on a 2 cmPepMap 100 C18 Nanotrap column (Dionex) at a flowrate of 4 μl/min for 10min. Separation was performed on either 25 cm or 50 cm PepMap C18columns with a particle size of 2 μm (Dionex) mounted in a column ovenrunning at 50° C. The applied gradient ranged from 3 to 32% solvent Bwithin 90 min at a flow rate of 300 nl/min (for 25 cm columns) or 140min at a flow rate of 175 nl/min (for 50 cm columns). (Solvent A: 99%H₂O, 1% ACN and 0.1% formic acid; Solvent B: 20% H₂O, 80% ACN and 0.1%formic acid).

Mass spectrometry analysis was performed in data dependent acquisitionmode employing a top five method (i.e. during each survey scan the fivemost abundant precursor ions were selected for fragmentation).Alternatively, a TopSpeed method was employed for analysis on FusionLumos instruments,

Survey scans were recorded in the Orbitrap at a resolution of 60,000(for Orbitrap XL) or 120,000 (for Orbitrap Fusion Lumos). MS/MS analysiswas performed by collision induced dissociation (CID, normalizedcollision energy 35%, activation time 30 ms, isolation width 1.3 m/z)with subsequent analysis in the linear trap quadrupole (LTQ). Mass rangefor HLA class I ligands was limited to 400-650 m/z with possible chargestates 2+ and 3+ selected for fragmentation. For HLA class II mass rangewas set to 300-1500 m/z allowing for fragmentation with all positivecharge states 2.

Tandem mass spectra were interpreted by MASCOT or SEQUEST at a fixedfalse discovery rate (q≤0.05) and additional manual control. In caseswhere the identified peptide sequence was uncertain it was additionallyvalidated by comparison of the generated natural peptide fragmentationpattern with the fragmentation pattern of a synthetic sequence-identicalreference peptide.

Table 19 shows the presentation on various cancer entities for selectedpeptides, and thus the particular relevance of the peptides as mentionedfor the diagnosis and/or treatment of the cancers as indicated (e.g.peptide SEQ ID No. 1 for colorectal cancer, gallbladder cancer,non-hodgkin lymphoma, non-small cell lung cancer, and uterine andendometrial cancer, peptide SEQ ID No. 2 for breast cancer,cholangiocellular carcinoma, colorectal cancer, gallbladder cancer,gastric cancer, head and neck squamous cell carcinoma, melanoma,non-hodgkin lymphoma, non-small cell lung cancer, esophageal cancer,pancreatic cancer, prostate cancer, renal cell carcinoma, small celllung cancer, and uterine and endometrial cancer).

TABLE 19  Overview of presentation of selected tumor-associated peptidesof the present invention across tumor types. Seq ID No SequencePeptide Presentation on tumor types 1 MIPTFTALLCRC, GBC, NHL, NSCLC, UEC 2 TLLKALLEI BRCA, CCC, CRC, GBC, GC, HNSCC,MEL, NHL, NSCLC, OSCAR, PACA, PRCA, RCC, SCLC, UEC 3 ALIYNLVG I HCC 4ALFKAWAL AML, BRCA, CLL, CRC, GBC, GC, HCC,HNSCC, MEL, NHL, NSCLC, OSCAR, RCC, SCLC, UBC, UEC 5 RLLDFINVL UEC 7ALQAFEFRV GC, GEJC, HNSCC, NSCLC, PACA, SCLC, UBCAML, BRCA, CCC, CLL, CRC, GBC, GBM, GC, GEJC, HCC, HNSCC, MEL,NHL, NSCLC, OSCAR, PACA, PRCA, 8 YLVTKVVAV RCC, SCLC, UBC, UEC 10RYSDSVGRVSF BRCA, CRC, GBC, GC, NSCLC, SCLC, UBC, UEC 11 SYSDLHYGFGC, NSCLC, UEC 12 KYEKIFEML AML, NSCLC 13 VYTFLSSTL NSCLC 14 FYFPTPTVLGBC, NSCLC 15 VYHDDKQPTF GBM, GC, NSCLC, OSCAR, UEC 16 IYSPQFSRLBRCA, NHL, NSCLC, OSCAR, UBC, UEC 18 KYPVHIYRLAML, BRCA, GBC, GC, HNSCC, MEL, NHL, NSCLC, OSCAR, PACA, RCC, UBC, UEC19 KYVKVFHQF AML, BRCA, CLL, CRC, GBC, GBM, GC,HCC, MEL, NHL, NSCLC, OSCAR, PACA, PRCA, RCC, SCLC, UBC, UEC 20RMASPVNVK CLL 21 AVRKPIVLK AML, BRCA, CCC, CRC, GBC, GBM,GC, HCC, HNSCC, MEL, NHL, NSCLC, OSCAR, PACA, RCC, SCLC, UBC, UEC 22SLKERNPLK NSCLC 24 SMYYPLQLK BRCA, CRC, GBM, HCC, NHL, RCC 25 GTSPPSVEKUEC 27 VLYGPAGLGK HCC, HNSCC, NSCLC, OSCAR, PACA, SCLC, UBC, UEC 28KTYETNLEIKK NSCLC, UBC 29 QQFLTALFY PACA, PRCA 31 LLDEGAMLLYGBC, HNSCC, NSCLC, SCLC, UBC 32 SPNKGTLSV NSCLC 33 SPTFHLTLNSCLC, PRCA, SCLC, UBC, UEC 34 LPRGPLASLLHNSCC, NSCLC, OSCAR, PACA, SCLC 35 FPDNQRPALBRCA, CRC, GBC, MEL, NSCLC, PACA, UBC, UEC 36 APAAWLRSABRCA, CCC, CRC, GBC, GC, HCC, HNSCC, NSCLC, OSCAR, PACA, SCLC, UBC, UEC38 SPHPVTALLTL PACA, UEC 40 KPGTSYRVTL GBM 43 ALKARTVTFBRCA, CCC, GBM, HCC, HNSCC, MEL, NHL, NSCLC, OSCAR, PRCA, SCLC, UBC, UEC48 DVKKKIKEV NSCLC, RCC, SCLC 53 MEHPGKLLF UEC 56 SEPDTTASW NSCLC, UECBRCA, CLL, CRC, GC, GEJC, HNSCC, 57 QESDLRLFL NHL, NSCLC, PACA, UBC, UEC59 SENVTMKVV UEC 60 GLLSLTSTLYL BRCA 62 KVLGVNVMLBRCA, HNSCC, MEL, NSCLC, SCLC 63 MMEEMIFNL UBC 64 FLDPDRHFLBRCA, CCC, CRC, GBC, GC, GEJC, HCC, HNSCC, MEL, NSCLC, OSCAR,PACA, PRCA, RCC, SCLC, UBC, UEC 65 TMFLRETSL MEL, NHL, NSCLC, PRCA, SCLC68 KLFDTQQFL AML, BRCA, CRC, HCC, HNSCC, MEL, NHL, NSCLC, OSCAR, RCC 69TTYEGSITV NSCLC, UEC 71 YLEDTDRNL AML, BRCA, CCC, CRC, GBC, GC,GEJC, HCC, HNSCC, MEL, NHL, NSCLC, OSCAR, PACA, PRCA, RCC,SCLC, UBC, UEC 72 YLTDLQVSL AML, BRCA, CCC, CLL, CRC, GBC,GBM, GC, GEJC, HCC, HNSCC, MEL, NHL, NSCLC, OSCAR, PACA, PRCA,RCC, SCLC, UBC, UEC 74 SQSPSVSQL UEC 75 KVVSVLYNV BRCA, UEC 77 RYGPVFTVCCC, GC 78 SFAPRSAVF SCLC 79 SYNEHWNYL BRCA, CCC, CRC, GBC, GC, HCC,HNSCC, MEL, NHL, NSCLC, OSCAR, PACA, PRCA, RCC, SCLC, UBC, UEC 81VYNHTTRPL OSCAR 85 VLLGSLFSRK AML, CRC, HCC, MEL, NHL, NSCLC, RCC, UEC86 VVLLGSLFSRK AML, CRC, GC, HCC, PACA, RCC 87 AVAPPTPASKAML, CRC, GBC, MEL, NSCLC, OSCAR, RCC, SCLC, UEC 90 KVAGERYVYK CCC, UEC92 SVFPIENIY UEC 94 ATFERVLLR BRCA, NSCLC 96 TAFGGFLKY OSCAR, RCC 97TMLDVEGLFY GC 99 KVVDRWNEK CRC, NHL, RCC 101 RVFTSSIKTK NSCLC, PACA, UEC106 AAFVPLLLK AML, BRCA, NHL, NSCLC, SCLC 108 VLYPVPLESYAML, MEL, NHL, NSCLC, RCC, SCLC, UEC 109 KTFTIKRFLAKBRCA, CCC, MEL, NHL, NSCLC, OSCAR, SCLC, UEC 110 SAAPPSYFR RCC, UEC 113QLDSNRLTY HCC 115 FVDNQYWRY BRCA, GBC, GC, GEJC, NSCLC,OSCAR, PACA, SCLC116 VLLDEGAMLLY NSCLC, PACA 117 APRLLLLAVL BRCA, CRC, HNSCC, MEL, NSCLC,OSCAR, PRCA, RCC, SCLC, UBC, UEC 118 SPASRSISL NHL, OSCAR, RCC 119APLPRPGAVL MEL, OSCAR 120 RPAMNYDKL CRC 123 KPSESIYSALBRCA, CRC, HNSCC, MEL, NHL, NSCLC, OSCAR, SCLC, UBC 124 LPSDSHFKITFCRC, HNSCC, NHL, OSCAR, SCLC 125 VPVYILLDEM CCC, GC, HNSCC, UEC 127APRAGSQVV AML, BRCA, CRC, GBM, HCC, HNSCC,MEL, NSCLC, OSCAR, PACA, PRCA, RCC, SCLC, UBC, UEC 129 APRPASSLBRCA, CRC, NSCLC, OSCAR, SCLC, UEC 133 MPNLPSTTSL UEC 141 SPMTSLLTSGLUEC 146 IPRPEVQAL AML, CRC, GC, HNSCC, MEL 147 APRWFPQPTVV BRCA 148KPYGGSGPL AML, BRCA, NHL, RCC 149 GPREALSRLAML, BRCA, CCC, CRC, HCC, MEL, NHL, NSCLC, OSCAR, PACA, PRCA,RCC, SCLC, UEC 150 MAAVKQAL CCC, NSCLC, PACA 151 HLLLKVLAF HNSCC 152MGSARVAEL HNSCC 156 HVKEKFLL CCC, HNSCC 157 EAMKRLSYI CCC, HNSCC, PACA174 AEATARLNVF NSCLC 176 AEIEPKADGSW CCC, NSCLC, PRCA 178 NELFRDGVNWAML, BRCA, CCC, CLL, CRC, HCC, HNSCC, MEL, NHL, NSCLC, OSCAR,PACA, PRCA, SCLC, UBC, UEC 179 REAGDEFEL CCC, NSCLC, SCLC 180REAGDEFELRY CRC, HCC, MEL, NSCLC, OSCAR, PACA, RCC, UEC 181 GEGPKTSWNSCLC 182 KEATEAQSL NSCLC 184 AELEALTDLW NHL, NSCLC, NSCLC 186 REGPEEPGLGC 188 AEFAKKQPWW CCC, CLL, CRC, MEL, NHL, NSCLC 191 EEDAALFKAWAML, BRCA, CCC, CLL, CRC, GC, HCC, HNSCC, MEL, NHL, NSCLC, OSCAR,PACA, PRCA, RCC, SCLC, UBC, UEC 192 YEFKFPNRLBRCA, HCC, NSCLC, OSCAR, UEC 196 REMPGGPVWBRCA, CCC, CRC, GC, HCC, HNSCC, MEL, NHL, NSCLC, OSCAR, PACA,SCLC, UBC, UEC 197 AEVLLPRLV NSCLC, PACA, UEC 199 REIDESLIFY NSCLC 200AESIPTVSF NSCLC 208 TEVSRTEAI NSCLC, UEC 211 EEKVFPSPLW NHL 215SEDGLPEGIHL CLL, GC, GEJC, HNSCC, NHL, NSCLC, PACA 216 IMFDDAIERA UEC217 VSSSLTLKV BRCA, RCC 224 SLPRFQVTL BRCA, HCC, NHL, NSCLC, OSCAR,UBC, UEC 225 SVFAHPRKL BRCA, OSCAR 226 QVDPKKRISM BRCA, NHL, NSCLC, SCLC227 YTFRYPLSL CCC, CRC, GBC, GC, HCC, HNSCC,NSCLC, OSCAR, PACA, SCLC, UBC, UEC 228 RLWDWVPLA AML, NHL 235 SAIETSAVLNSCLC, UEC 237 SAMGTISIM UEC 240 FSTDTSIVL PACA 241 RQPNILVHL UEC 243YASEGVKQV UEC 245 LAVEGGQSL AML, BRCA, CCC, CRC, GBC, GBM,GC, GEJC, HCC, HNSCC, MEL, NHL, NSCLC, OSCAR, PACA, PRCA, RCC,SCLC, UBC, UEC 246 RYLAVVHAVF HCC, NHL, NSCLC, PACA, SCLC 247 ARPPWMWVLBRCA, GBC, HNSCC, OSCAR 251 KQRQVLIFF GBM, NSCLC, OSCAR, PACA, RCC 252LYQPRASEM NHL 256 RTEEVLLTFK RCC, SCLC, UEC 257 VTADHSHVF UEC 259KTLELRVAY GBC, HNSCC 260 GTNTVILEY MEL, PACA, UEC 262 RSRLNPLVQRHNSCC, NSCLC 264 AIKVIPTVFK HNSCC, MEL, NSCLC, RCC, UEC 268 GLLGLSLRYPRCA 269 RLKGDAWVYK MEL, NHL, OSCAR, UEC 271 RMFADDLHNLNK NSCLC 273RVNAIPFTY GBC 275 STTFPTLTK UEC 277 TTALKTTSR NSCLC 279 SVSSETTKIKR UEC280 SVSGVKTTF HCC, UEC 281 RAKELEATF CLL, GC, NSCLC 283 IVQEPTEEKHCC, NHL, NSCLC 286 TVAPPQGVVK HCC 288 SPVTSVHGGTY NHL 289 RWEKTDLTYCRC, UEC 291 ETIRSVGYY GBM, NSCLC, UBC 295 YPLRGSSIFGL UEC 296 YPLRGSSIUEC 299 HPGSSALHY AML, CCC, CRC, GC, HNSCC, MEL,NHL, NSCLC, OSCAR, PACA, PRCA, RCC, UEC 300 IPMAAVKQALAML, BRCA, CLL, CRC, GC, HCC, HNSCC, MEL, NSCLC, OSCAR, PACA, RCC, UEC302 RVEEVRALL BRCA, CRC, GBM, UBC 306 APVIFSHSAAML, CCC, HCC, MEL, NSCLC, UBC 307 LPYGPGSEAAAF BRCA, UEC 308 YPEGAAYEFPRCA, UEC 314 VPDQPHPEI PACA 315 SPRENFPDTL HNSCC 317 FPFQPGSVAML, BRCA, CLL, CRC, GBC, GBM, GC, HCC, HNSCC, MEL, NHL, NSCLC,OSCAR, PACA, PRCA, RCC, SCLC, UBC, UEC 318 FPNRLNLEACCC, CLL, GC, HNSCC, MEL, NSCLC, PRCA, RCC, SCLC, UBC 319 SPAEPSVYATLBRCA, GC, NSCLC, OSCAR 320 FPMSPVTSV AML, BRCA, CCC, CRC, GBC, GBM,GC, HCC, HNSCC, MEL, NHL, NSCLC, OSCAR, PACA, PRCA, RCC, SCLC, UBC, UEC321 SPMDTFLLI AML, BRCA, CLL, CRC, GBC, GBM, GC,HCC, HNSCC, MEL, NHL, NSCLC, OSCAR, PACA, PRCA, RCC, SCLC, UBC, UEC 322SPDPSKHLL NHL, NSCLC, PRCA, RCC 324 VPYRVVGLCLL, CRC, GC, MEL, NHL, NSCLC, PRCA, SCLC 325 GPRNAQRVLCRC, GBC, NHL, NSCLC 326 VPSEIDAAF BRCA, CCC, CRC, GBC, GC, NSCLC,OSCAR, PACA, RCC, SCLC, UEC 330 FPFVTGSTEM UEC 331 FPHPEMTTSM UEC 332FPHSEMTTL NSCLC, PACA 333 FPHSEMTTVM NSCLC, SCLC, UEC 334 FPYSEVTTLNSCLC, SCLC, UEC 335 HPDPVGPGL NSCLC, UEC 337 HPVETSSAL UEC 355SPLVTSHIM UEC 363 TAKTPDATF CCC 369 FPHSEMTTV PACA, UEC 371 LYVDGFTHWNSCLC, UEC 376 RPRSPAGQVA PACA 378 RPRSPAGQVAA NHL, PACA, SCLC 385SPALHIGSV BRCA, GBM, HCC, NSCLC, PRCA, SCLC, UBC, UEC 386 FPFNPLDFGC, NHL 388 SPAPLKLSRTPA MEL 389 SPGAQRTFFQL AML, MEL 391 APSTPRITTFHCC, NHL 392 KPIESTLVA GBM, MEL, NSCLC, UEC 393 ASKPHVEI CRC 395VLLPRLVSC NSCLC 399 RELLHLVTL NSCLC, SCLC, UEC 403 EEAQWVRKYBRCA, CLL, NHL 404 NEAIMHQY BRCA, CCC, CLL, CRC, GBC, GC, HCC,MEL, NHL, NSCLC, OSCAR, SCLC, UBC, UEC 405 NEIWTHSY NSCLC, UEC 407AEHEGVSVL NSCLC, UEC 408 LEKALQVF CRC, GC, HNSCC, OSCAR, UEC 409REFVLSKGDAGL GBC, GC, GEJC, HNSCC, NSCLC 410 SEDPSKLEABRCA, HNSCC, NSCLC, OSCAR, SCLC, UEC 411 LELPPILVYBRCA, CRC, GBC, GBM, GC, NHL, NSCLC, OSCAR, PRCA, SCLC, UBC, UEC 414EDAALFKAW CLL, CRC, MEL, NHL 415 REEDAALFKAWBRCA, CLL, CRC, HCC, HNSCC, MEL, NHL, NSCLC, OSCAR, PRCA, UBC, UEC 416SEEETRVVF AML, CRC, HNSCC, NSCLC, UEC 417 AEHFSMIRAAML, BRCA, CRC, GBM, GC, HNSCC, NHL, NSCLC, OSCAR, PACA, PRCA, RCC, UEC418 FEDAQGHIW BRCA, CCC, CRC, HCC, NSCLC, OSCAR, PACA, UBC, UEC 419HEFGHVLGL BRCA, CCC, CRC, GC, HNSCC, MEL, NSCLC, OSCAR, PACA, UEC 420FESHSTVSA UEC 423 SEVPTGTTA GBC, GBM 425 SEVPLPMAI NSCLC, UEC 429REKFIASVI UEC 430 DEKILYPEF UEC 431 AEQDPDELNKA CRC, OSCAR, SCLC, UEC432 EEQYIAQF OSCAR, SCLC 433 SDSQVRAF GBM, GC, HCC, HNSCC, NSCLC,OSCAR, RCC, SCLC, UEC 436 REPGDIFSEL CRC 437 TEAVVTNELCRC, GC, NSCLC, SCLC, UEC 438 SEVDSPNVL CCC, CLL, CRC, GC, HNSCC, MEL,NHL, NSCLC, SCLC, UBC 442 ILSKLTDIQY BRCA, GBM, NHL, NSCLC 443 GTFNPVSLWBRCA, GBC, GBM, HNSCC, MEL, NHL, NSCLC, OSCAR, PACA, SCLC 444 KLSQKGYSWBRCA, CCC, CRC, GBM, HCC, HNSCC, MEL, NHL, NSCLC, OSCAR, PACA,PRCA, SCLC, UBC 445 LHITPGTAY HCC, PRCA 446 GRIVAFFSFAML, BRCA, CRC, HCC, HNSCC, MEL, NHL, NSCLC, OSCAR, PACA, PRCA,SCLC, UBC, UEC 447 MQVLVSRI GC, NSCLC, PACA, PRCA, RCC, SCLC 448LSQKGYSW NHL, NSCLC, UBC 451 DYLNEWGSRF NSCLC, OSCAR, UEC 454 AQTDPTTGYGBM, GC, NSCLC 455 AAAANAQVY BRCA, UEC 456 IPLERPLGEVY BRCA, UEC 457NAAAAANAQVY BRCA, NSCLC, UEC 458 TDTLIHLM UEC 459 KVAGERYVYBRCA, CCC, CRC, GBM, HNSCC, MEL, NSCLC, OSCAR, PACA, PRCA, SCLC, UBC 460RLSSATANALY GBC 461 AQRMTTQLL CRC, MEL, NSCLC, RCC 462 QRMTTQLLLNSCLC, RCC, UEC 466 DLIESGQLRER UEC 467 MQMQERDTLGEJC, HNSCC, NHL, NSCLC, OSCAR 471 AQRLDPVYF CCC, CRC, GBC, GEJC, NSCLC,OSCAR, PACA, SCLC, UBC 472 MRLLVAPL SCLC, UEC 474 AADGGLRASVTLBRCA, NSCLC, OSCAR 477 RIQQQTNTY GBM, SCLC 479 TEGSHFVEA BRCA, SCLC, UEC480 GRADIMIDF BRCA, CRC, HNSCC, MEL, NSCLC, OSCAR, SCLC, UEC 481GRWEKTDLTY BRCA, GBC, HNSCC, MEL, NSCLC, OSCAR, PACA, SCLC, UBC, UEC 482GRWEKTDLTYR HNSCC, NSCLC, OSCAR, PACA, SCLC, UEC 484 AWLRSAAA CCC 485VRFPVHAAL MEL, NSCLC, OSCAR 486 DRFFWLKV NSCLC, SCLC 487 GMADILVVF NSCLC488 RSFSLGVPR AML, CLL, GC, HCC, HNSCC, NHL, NSCLC, PRCA, SCLC, UEC 490AEVQKLLGP HNSCC, NSCLC, OSCAR, UEC 491 EAYSSTSSW GBC, UEC 493 DTNLEPVTRUEC 495 EVPSGATTEVSR UEC 496 EVPTGTTAEVSR UEC 498 EVYPELGTQGR UEC 503TVFDKAFTAA NSCLC 507 TSIFSGQSL UEC 508 TVAKTTTTF UEC 509 GRGPGGVSW NSCLC518 TSDFPTITV PACA 520 THSAMTHGF NHL 527 QSTPYVNSV UEC 528 TRTGLFLRFHNSCC, NSCLC, UEC 533 GQHLHLETF AML, CCC, GBC, GC, HCC, MEL, NHL,NSCLC, OSCAR, RCC, SCLC, UBC, UEC 537 IRRLKELKDQ NSCLC 539 IPIPSTGSVEMCCC, GC, HNSCC, NSCLC, OSCAR, PRCA, SCLC, UBC, UEC 540 AGIPAVALWHCC, NSCLC, OSCAR 541 RLSPAPLKL GBM, NSCLC 544 LRNPSIQKL GBM 545RVGPPLLI BRCA, CRC, NSCLC, OSCAR, UEC 546 GRAFFAAAFCRC, GBM, HNSCC, MEL, NSCLC, OSCAR, PACA, SCLC, UBC, UEC 547 EVNKPGVYTRHCC, UEC 549 ARSKLQQGL MEL 550 RRFKEPWFL BRCA, HCC, MEL, NSCLC, PRCA,SCLC, UBC, UEC 563 PNFSGNWKIIRSENFEEL NSCLC 589 APDAKSFVLNLGKDSNNL NSCLC590 RVRGEVAPDAKSFVLNLG NSCLC 591 VRGEVAPDAKSFVLNL NSCLC, RCC 592VRGEVAPDAKSFVLNLG NSCLC, RCC 593 GEVAPDAKSFVLNLG NSCLC, RCC 594VRGEVAPDAKSFVLN NSCLC, RCC 598 AESLFREALSNKVDEL NSCLC 599AESLFREALSNKVDE NSCLC 607 LTVAEVQKLLGPHVEGLKAEE NSCLC 608LTVAEVQKLLGPHVEGLKAE NSCLC 609 LTVAEVQKLLGPHVEGLKA NSCLC 610LTVAEVQKLLGPHVEGLK NSCLC 611 LTVAEVQKLLGPHVEGL NSCLC 612TVAEVQKLLGPHVEGLK NSCLC 613 LTVAEVQKLLGPHVEG NSCLC 614 TVAEVQKLLGPHVEGLNSCLC 615 VAEVQKLLGPHVEGLK NSCLC 616 TVAEVQKLLGPHVEG NSCLC 617VAEVQKLLGPHVEGL NSCLC 618 VAEVQKLLGPHVEG NSCLC 619 VAEVQKLLGPHVE NSCLC620 EVQKLLGPHVEG NSCLC 625 DALRGLLPVLGQPIIRSIPQG NSCLC 628DALRGLLPVLGQPIIRSIPQ NSCLC 629 GLLPVLGQPIIRSIPQGIVA NSCLC 630ALRGLLPVLGQPIIRSIPQ NSCLC 633 LRGLLPVLGQPIIRSIPQ NSCLC 634DALRGLLPVLGQPIIRS NSCLC 635 ALRGLLPVLGQPIIRS NSCLC 637 ALRGLLPVLGQPIIRNSCLC 638 LRGLLPVLGQPIIRS NSCLC 639 ALRGLLPVLGQPII NSCLC 646GLLPVLGQPIIRSIPQGIVAAWRQ NSCLC 648 GLLPVLGQPIIRSIPQGIVAA NSCLC 651LPVLGQPIIRSIPQGIVAA NSCLC 653 LPVLGQPIIRSIPQGIVA NSCLC 654PVLGQPIIRSIPQGIVA GC, NSCLC 656 VLGQPIIRSIPQGIVA NSCLC 661LRGLLPVLGQPIIRSIPQG NSCLC 666 LPLTVAEVQKLLGPHVEG NSCLC 668 AVLPLTVAEVQKBRCA, CRC, GBC, GC, NSCLC, PACA, UEC 677 IWAVRPQDLDTCDPR NSCLC 680GVRGSLLSEADVRALGGLA NSCLC 682 GVRGSLLSEADVRALGGL NSCLC 686VRGSLLSEADVRALGGL NSCLC 694 GSLLSEADVRALGG NSCLC 695 RGSLLSEADVRALGNSCLC 697 GSLLSEADVRALG NSCLC 717 IPQGIVAAWRQRSSRDPS GC 730LPGRFVAESAEVL NSCLC AML: acute myeloid leukemia; BRCA: breast cancer;CCC: cholangiocellular carcinoma; CLL: chronic lymphocytic leukemia;CRC: colorectal cancer; GBC: gallbladder cancer; GBM: glioblastoma; GC:gastric cancer; GEJC: gastro-esophageal junction cancer; HCC:hepatocellular carcinoma; HNSCC: head and neck squamous cell carcinoma;MEL: melanoma; NHL: non-hodgkin lymphoma; NSCLC: non-small cell lungcancer; OC: ovarian cancer; OSCAR: esophageal cancer; PACA: pancreaticcancer; PRCA: prostate cancer; RCC: renal cell carcinoma; SCLC: smallcell lung cancer; UBC: urinary bladder carcinoma; UEC: uterine andendometrial cancer

Example 2

Expression Profiling of Genes Encoding the Peptides of the Invention

Over-presentation or specific presentation of a peptide on tumor cellscompared to normal cells is sufficient for its usefulness inimmunotherapy, and some peptides are tumor-specific despite their sourceprotein occurring also in normal tissues. Still, mRNA expressionprofiling adds an additional level of safety in selection of peptidetargets for immunotherapies. Especially for therapeutic options withhigh safety risks, such as affinity-matured TCRs, the ideal targetpeptide will be derived from a protein that is unique to the tumor andnot found on normal tissues.

RNA Sources and Preparation

Surgically removed tissue specimens were provided as indicated above(see Example 1) after written informed consent had been obtained fromeach patient. Tumor tissue specimens were snap-frozen immediately aftersurgery and later homogenized with mortar and pestle under liquidnitrogen. Total RNA was prepared from these samples using TRI Reagent(Ambion, Darmstadt, Germany) followed by a cleanup with RNeasy (QIAGEN,Hilden, Germany); both methods were performed according to themanufacturer's protocol.

Total RNA from healthy human tissues for RNASeq experiments was obtainedfrom: Asterand (Detroit, Mich., USA & Royston, Herts, UK); Bio-OptionsInc. (Brea, Calif., USA); Geneticist Inc. (Glendale, Calif., USA);ProteoGenex Inc. (Culver City, Calif., USA); Tissue Solutions Ltd(Glasgow, UK).

Total RNA from tumor tissues for RNASeq experiments was obtained from:Asterand (Detroit, Mich., USA & Royston, Herts, UK); BioCat GmbH(Heidelberg, Germany); BioServe (Beltsville, Md., USA); Geneticist Inc.(Glendale, Calif., USA); Istituto Nazionale Tumori “Pascale” (Naples,Italy); ProteoGenex Inc. (Culver City, Calif., USA); University HospitalHeidelberg (Heidelberg, Germany).

Quality and quantity of all RNA samples were assessed on an Agilent 2100Bioanalyzer (Agilent, Waldbronn, Germany) using the RNA 6000 PicoLabChip Kit (Agilent).

RNAseq Experiments

Gene expression analysis of—tumor and normal tissue RNA samples wasperformed by next generation sequencing (RNAseq) by CeGaT (Tübingen,Germany). Briefly, sequencing libraries are prepared using the IlluminaHiSeq v4 reagent kit according to the provider's protocol (IlluminaInc., San Diego, Calif., USA), which includes RNA fragmentation, cDNAconversion and addition of sequencing adaptors. Libraries derived frommultiple samples are mixed equimolar and sequenced on the Illumina HiSeq2500 sequencer according to the manufacturer's instructions, generating50 bp single end reads. Processed reads are mapped to the human genome(GRCh38) using the STAR software. Expression data are provided ontranscript level as RPKM (Reads Per Kilobase per Million mapped reads,generated by the software Cufflinks) and on exon level (total reads,generated by the software Bedtools), based on annotations of the ensemblsequence database (Ensembl77). Exon reads are normalized for exon lengthand alignment size to obtain RPKM values.

Exemplary expression profiles of source genes of the present inventionthat are highly over-expressed or exclusively expressed in ovariancancer are shown in FIGS. 1A through 1V. Expression scores for furtherexemplary genes are shown in Table 10.

TABLE 10  Expression scores. Seq ID No Sequence Gene Expression 1MIPTFTALL ++ 5 RLLDFINVL +++ 6 SLGKHTVAL +++ 10 RYSDSVGRVSF + 11SYSDLHYGF ++ 12 KYEKIFEML +++ 13 VYTFLSSTL +++ 14 FYFPTPTVL ++ 16IYSPQFSRL +++ 17 RFTTMLSTF +++ 18 KYPVHIYRL + 20 RMASPVNVK ++ 21AVRKPIVLK + 22 SLKERNPLK ++ 23 GMMKGGIRK +++ 25 GTSPPSVEK ++ 26RISEYLLEK +++ 27 VLYGPAGLGK +++ 28 KTYETNLEIKK +++ 29 QQFLTALFY +++ 30ALEVAHRLK + 31 LLDEGAMLLY +++ 32 SPNKGTLSV + 33 SPTFHLTL + 34 LPRGPLASLL++ 35 FPDNQRPAL ++ 36 APAAWLRSA +++ 37 RPLFQKSSM +++ 38 SPHPVTALLTL ++39 RPAPFEVVF ++ 40 KPGTSYRVTL +++ 42 TLKVTSAL + 43 ALKARTVTF + 47MPNLRSVDL +++ 51 SLRLKNVQL +++ 52 AEFLLRIFL + 53 MEHPGKLLF +++ 54AEITITTQTGY ++ 55 HETETRTTW ++ 56 SEPDTTASW ++ 57 QESDLRLFL +++ 58GEMEQKQL +++ 59 SENVTMKVV +++ 60 GLLSLTSTLYL + 61 YMVHIQVTL ++ 62KVLGVNVML ++ 63 MMEEMIFNL ++ 64 FLDPDRHFL ++ 66 GLLQELSSI +++ 67SLLLPSIFL +++ 69 TTYEGSITV ++ 70 VLQGLLRSL +++ 71 YLEDTDRNL + 72YLTDLQVSL + 73 FLIEELLFA +++ 74 SQSPSVSQL +++ 75 KVVSVLYNV +++ 76KYVAELSLL +++ 77 RYGPVFTV +++ 78 SFAPRSAVF ++ 82 SYFRGFTLI +++ 83GTYAHTVNR +++ 84 KLQPAQTAAK +++ 87 AVAPPTPASK ++ 88 VVHAVFALK + 89RVAELLLLH +++ 90 KVAGERYVYK ++ 91 RSLRYYYEK ++ 92 SVFPIENIY ++ 96TAFGGFLKY +++ 97 TMLDVEGLFY ++ 98 LLQPPPLLAR +++ 100 RLFTSPIMTK ++ 101RVFTSSIKTK ++ 102 SVLTSSLVK ++ 103 TSRSVDEAY ++ 104 VLADSVTTK ++ 107RLQEWKALK +++ 108 VLYPVPLESY +++ 110 SAAPPSYFR +++ 111 TLPQFRELGY ++ 112TVTGAEQIQY ++ 113 QLDSNRLTY ++ 114 VMEQSAGIMY +++ 115 FVDNQYWRY +++ 116VLLDEGAMLLY +++ 117 APRLLLLAVL ++ 118 SPASRSISL ++ 119 APLPRPGAVL +++120 RPAMNYDKL ++ 121 VPNQSSESL +++ 122 YPGFPQSQY +++ 123 KPSESIYSAL +++124 LPSDSHFKITF +++ 125 VPVYILLDEM ++ 126 KPGPEDKL ++ 128 YPRTITPGM +129 APRPASSL ++ 130 FPRLVGPDF + 131 APTEDLKAL ++ 132 IPGPAQSTI ++ 133MPNLPSTTSL ++ 135 RVRSTISSL ++ 136 SPFSAEEANSL ++ 137 SPGATSRGTL ++ 138SPMATTSTL ++ 139 SPQSMSNTL ++ 140 SPRTEASSAVL ++ 141 SPMTSLLTSGL ++ 142TPGLRETSI ++ 143 SPAMTSTSF ++ 144 SPSPVSSTL ++ 145 SPSSPMSTF ++ 147APRWFPQPTVV +++ 151 HLLLKVLAF +++ 152 MGSARVAEL +++ 154 MLRKIAVAA ++ 155NKKMMKRLM +++ 156 HVKEKFLL ++ 157 EAMKRLSYI + 159 VLKHKLDEL ++ 160YPKARLAF ++ 161 ALKTTTTAL ++ 162 QAKTHSTL ++ 163 QGLLRPVF +++ 164SIKTKSAEM ++ 165 SPRFKTGL ++ 166 TPKLRETSI ++ 167 TSHERLTTL ++ 168TSHERLTTY ++ 169 TSMPRSSAM ++ 170 YLLEKSRVI +++ 171 FAFRKEAL +++ 172KLKERNREL +++ 173 AEAQVGDERDY + 174 AEATARLNVF + 175 AEIEPKADG + 176AEIEPKADGSW + 177 TEVGTMNLF ++ 181 GEGPKTSW + 183 YEKGIMQKV ++ 184AELEALTDLW ++ 185 AERQPGAASL ++ 186 REGPEEPGL ++ 187 GEAQTRIAW ++ 189KEFLFNMY ++ 190 YEVARILNL ++ 193 LEAQQEAL ++ 194 KEVDPTSHSY +++ 195AEDKRHYSV + 196 REMPGGPVW +++ 197 AEVLLPRLV ++ 198 QEAARAAL ++ 199REIDESLIFY ++ 200 AESIPTVSF ++ 201 AETILTFHAF ++ 202 HESEATASW ++ 203IEHSTQAQDTL ++ 204 RETSTSEETSL ++ 205 SEITRIEM ++ 206 SESVTSRTSY +++ 207TEARATSDSW ++ 208 TEVSRTEAI ++ 209 TEVSRTEL ++ 210 VEAADIFQNF ++ 211EEKVFPSPLW +++ 212 MEQKQLQKRF +++ 214 VEQTRAGSLL ++ 216 IMFDDAIERA +++217 VSSSLTLKV + 218 TIASQRLTPL ++ 219 PLPRPGAVL +++ 220 RMTTQLLLL ++ 225SVFAHPRKL ++ 226 QVDPKKRISM ++ 227 YTFRYPLSL ++ 229 ISVPAKTSL ++ 230SAFREGTSL ++ 231 SVTESTHHL ++ 232 TISSLTHEL ++ 233 GSDTSSKSL ++ 234GVATRVDAI +++ 235 SAIETSAVL ++ 236 SAIPFSMTL ++ 237 SAMGTISIM ++ 238PLLVLFTI +++ 239 FAVPTGISM ++ 240 FSTDTSIVL ++ 241 RQPNILVHL ++ 242STIPALHEI ++ 243 YASEGVKQV ++ 244 DTDSSVHVQV ++ 246 RYLAVVHAVF + 247ARPPWMWVL +++ 248 SVIQHLGY ++ 249 VYTPTLGTL ++ 250 HFPEKTTHSF ++ 252LYQPRASEM +++ 254 IIQHLTEQF +++ 255 VFVSFSSLF +++ 256 RTEEVLLTFK ++ 257VTADHSHVF +++ 258 GAYAHTVNR +++ 259 KTLELRVAY + 260 GTNTVILEY ++ 261HTFGLFYQR ++ 262 RSRLNPLVQR ++ 263 SSSSATISK ++ 266 ISYSGQFLVK +++ 267VTDLISPRK +++ 268 GLLGLSLRY +++ 269 RLKGDAWVYK ++ 270 AVFNPRFYRTY +++272 RQPERTILRPR ++ 273 RVNAIPFTY ++ 274 KTFPASTVF ++ 275 STTFPTLTK ++276 VSKTTGMEF ++ 277 TTALKTTSR ++ 278 NLSSITHER ++ 279 SVSSETTKIKR ++280 SVSGVKTTF ++ 281 RAKELEATF +++ 282 CLTRTGLFLRF +++ 285 GTVNPTVGK ++286 TVAPPQGVVK + 287 RRIHTGEKPYK ++ 288 SPVTSVHGGTY + 289 RWEKTDLTY ++290 DMDEEIEAEY +++ 291 ETIRSVGYY ++ 292 NVTMKVVSVLY +++ 293 VPDSGATATAY+++ 294 YPLRGSSIF +++ 295 YPLRGSSIFGL +++ 296 YPLRGSSI +++ 297TVREASGLL + 298 YPTEHVQF + 299 HPGSSALHY ++ 301 SPRRSPRISF + 302RVEEVRALL +++ 303 LPMWKVTAF +++ 304 LPRPGAVL +++ 305 TPWAESSTKF ++ 306APVIFSHSA ++ 307 LPYGPGSEAAAF +++ 308 YPEGAAYEF +++ 309 FPQSQYPQY +++310 RPNPITIIL +++ 311 RPLFYVVSL +++ 312 LPYFREFSM +++ 313 KVKSDRSVF +++315 SPRENFPDTL +++ 316 EPKTATVL ++ 320 FPMSPVTSV + 321 SPMDTFLLI + 322SPDPSKHLL + 323 RPMPNLRSV +++ 324 VPYRVVGL +++ 326 VPSEIDAAF ++ 327SPLPVTSLI ++ 328 EPVTSSLPNF ++ 329 FPAMTESGGMIL ++ 330 FPFVTGSTEM ++ 331FPHPEMTTSM ++ 332 FPHSEMTTL ++ 333 FPHSEMTTVM ++ 334 FPYSEVTTL ++ 335HPDPVGPGL +++ 336 HPKTESATPAAY ++ 337 HPVETSSAL ++ 338 HVTKTQATF ++ 339LPAGTTGSLVF ++ 340 LPEISTRTM ++ 341 LPLDTSTTL ++ 342 LPLGTSMTF ++ 343LPSVSGVKTTF ++ 344 LPTQTTSSL ++ 345 LPTSESLVSF ++ 346 LPWDTSTTLF ++ 347MPLTTGSQGM ++ 348 MPNSAIPFSM ++ 349 MPSLSEAMTSF ++ 350 NPSSTTTEF ++ 351NVLTSTPAF ++ 352 SPAETSTNM ++ 353 SPAMTTPSL ++ 354 SPLPVTSLL ++ 355SPLVTSHIM ++ 356 SPNEFYFTV ++ 357 SPSPVPTTL ++ 358 SPSPVTSTL ++ 359SPSTIKLTM ++ 360 SPSVSSNTY ++ 361 SPTHVTQSL ++ 362 SPVPVTSLF ++ 363TAKTPDATF ++ 364 TPLATTQRF ++ 365 TPLATTQRFTY ++ 366 TPLTTTGSAEM ++ 367TPSVVTEGF ++ 368 VPTPVFPTM ++ 369 FPHSEMTTV ++ 370 PGGTRQSL ++ 372IPRNPPPTLL +++ 373 RPRALRDLRIL +++ 374 NPIGDTGVKF +++ 375 AAASPLLLL +++376 RPRSPAGQVA +++ 377 RPRSPAGQVAAA +++ 378 RPRSPAGQVAA +++ 379GPFPLVYVL +++ 380 IPTYGRTF +++ 381 LPEQTPLAF +++ 382 SPMHDRWTF +++ 383TPTKETVSL +++ 384 YPGLRGSPM +++ 387 APLKLSRTPA +++ 388 SPAPLKLSRTPA +++389 SPGAQRTFFQL ++ 395 VLLPRLVSC ++ 396 REASGLLSL + 397 REGDTVQLL + 399RELLHLVTL + 400 GEIEIHLL + 403 EEAQWVRKY ++ 404 NEAIMHQY ++ 405 NEIWTHSY++ 411 LELPPILVY + 412 QEILTQVKQ +++ 413 lEALSGKIEL +++ 416 SEEETRVVF ++417 AEHFSMIRA +++ 418 FEDAQGHIW ++ 419 HEFGHVLGL ++ 420 FESHSTVSA ++ 421GEPATTVSL ++ 422 SETTFSLIF ++ 423 SEVPTGTTA ++ 424 TEFPLFSAA ++ 425SEVPLPMAI ++ 426 PEKTTHSF ++ 427 HESSSHHDL + 428 LDLGLNHI ++ 429REKFIASVI +++ 430 DEKILYPEF +++ 432 EEQYIAQF +++ 433 SDSQVRAF +++ 435REEFVSIDHL +++ 436 REPGDIFSEL +++ 437 TEAVVTNEL + The table listspeptides from genes that are very highly over-expressed in OC tumorscompared to a panel of normal tissues (+++), highly over-expressed in OCtumors compared to a panel of normal tissues (++) or over-expressed inOC tumors compared to a panel of normal tissues (+). The baseline forthis score was calculated from measurements of the following relevantnormal tissues: adipose tissue, adrenal gland, bile duct, blood cells,blood vessels, bone marrow, brain, cartilage, large intestine, liver,lung, lymph esophagus, eye, gallbladder, heart, head&neck, kidney, node,nerve, parathyroid, pancreas, pituitary, skeletal muscle, skin, smallintestine, spleen, stomach, thyroid gland, trachea, urinary bladder. Incase expression data for several samples of the same tissue type wereavailable, the arithmetic mean of all respective samples was used forthe calculation.

Example 3

In Vitro Immunogenicity for MHC Class I Presented Peptides

In order to obtain information regarding the immunogenicity of theTUMAPs of the present invention, the inventors performed investigationsusing an in vitro T-cell priming assay based on repeated stimulations ofCD8+ T cells with artificial antigen presenting cells (aAPCs) loadedwith peptide/MHC complexes and anti-CD28 antibody. This way theinventors could show immunogenicity for HLA-A*0201, HLA-A*24:02,HLA-A*01:01, HLA-A*03:01, HLA-B*07:02 and HLA-B*44:02 restricted TUMAPsof the invention, demonstrating that these peptides are T-cell epitopesagainst which CD8+ precursor T cells exist in humans (Table 11).

In Vitro Priming of CD8+ T Cells

In order to perform in vitro stimulations by artificial antigenpresenting cells loaded with peptide-MHC complex (pMHC) and anti-CD28antibody, the inventors first isolated CD8+ T cells from fresh HLA-A*02,HLA-A*24, HLA-A*01, HLA-A*03, HLA-B*07 or HLA-B*44 leukapheresisproducts via positive selection using CD8 microbeads (Miltenyi Biotec,Bergisch-Gladbach, Germany) of healthy donors obtained from theUniversity clinics Mannheim, Germany, after informed consent.

PBMCs and isolated CD8+ lymphocytes were incubated in T-cell medium(TCM) until use consisting of RPMI-Glutamax (Invitrogen, Karlsruhe,Germany) supplemented with 10% heat inactivated human AB serum(PAN-Biotech, Aidenbach, Germany), 100 U/ml Penicillin/100 μg/mlStreptomycin (Cambrex, Cologne, Germany), 1 mM sodium pyruvate (CC Pro,Oberdorla, Germany), 20 μg/ml Gentamycin (Cambrex). 2.5 ng/ml IL-7(PromoCell, Heidelberg, Germany) and 10 U/ml IL-2 (Novartis Pharma,Nürnberg, Germany) were also added to the TCM at this step.

Generation of pMHC/anti-CD28 coated beads, T-cell stimulations andreadout was performed in a highly defined in vitro system using fourdifferent pMHC molecules per stimulation condition and 8 different pMHCmolecules per readout condition.

The purified co-stimulatory mouse IgG2a anti human CD28 Ab 9.3 (Jung etal., 1987) was chemically biotinylated usingsulfo-N-hydroxysuccinimidobiotin as recommended by the manufacturer(Perbio, Bonn, Germany). Beads used were 5.6 μm diameter streptavidincoated polystyrene particles (Bangs Laboratories, Illinois, USA).

pMHC used for positive and negative control stimulations wereA*0201/MLA-001 (peptide ELAGIGILTV (SEQ ID NO. 775) from modifiedMelan-A/MART-1) and A*0201/DDX5-001 (YLLPAIVHI from DDX5, SEQ ID NO.776), respectively.

800.000 beads/200 μl were coated in 96-well plates in the presence of4×12.5 ng different biotin-pMHC, washed and 600 ng biotin anti-CD28 wereadded subsequently in a volume of 200 μl. Stimulations were initiated in96-well plates by co-incubating 1×10⁶ CD8+ T cells with 2×10⁶ washedcoated beads in 200 μl TCM supplemented with 5 ng/ml IL-12 (PromoCell)for 3 days at 37° C. Half of the medium was then exchanged by fresh TCMsupplemented with 80 U/ml IL-2 and incubating was continued for 4 daysat 37° C. This stimulation cycle was performed for a total of threetimes. For the pMHC multimer readout using 8 different pMHC moleculesper condition, a two-dimensional combinatorial coding approach was usedas previously described (Andersen et al., 2012) with minor modificationsencompassing coupling to 5 different fluorochromes. Finally, multimericanalyses were performed by staining the cells with Live/dead near IR dye(Invitrogen, Karlsruhe, Germany), CD8-FITC antibody clone SK1 (BD,Heidelberg, Germany) and fluorescent pMHC multimers. For analysis, a BDLSRII SORP cytometer equipped with appropriate lasers and filters wasused. Peptide specific cells were calculated as percentage of total CD8+cells. Evaluation of multimeric analysis was done using the FlowJosoftware (Tree Star, Oregon, USA). In vitro priming of specificmultimer+CD8+ lymphocytes was detected by comparing to negative controlstimulations. Immunogenicity for a given antigen was detected if atleast one evaluable in vitro stimulated well of one healthy donor wasfound to contain a specific CD8+ T-cell line after in vitro stimulation(i.e. this well contained at least 1% of specific multimer+ among CD8+T-cells and the percentage of specific multimer+ cells was at least 10×the median of the negative control stimulations).

In Vitro Immunogenicity for Ovarian Cancer Peptides

For tested HLA class I peptides, in vitro immunogenicity could bedemonstrated by generation of peptide specific T-cell lines. Exemplaryflow cytometry results after TUMAP-specific multimer staining for 14peptides of the invention are shown in FIGS. 2 through 9B together withcorresponding negative controls. Results for 118 peptides from theinvention are summarized in Table 11 a and Table 11b.

TABLE 11a  in vitro immunogenicity of HLA class I peptides of the invention. Exemplary results of in vitro immunogenicity experiments conducted by the applicant for the peptides of the invention.<20% = +; 20%-49% = ++; 50%-69% = +++;  >=70% = ++++  Seq ID SequenceWells positive [%] 773 ALYGKLLKL +++ 774 VYVDDIYVI +++

TABLE 11b  in vitro immunogenicity of HLA class I peptidesof the invention. Exemplary results of in vitroimmunogenicity experiments conducted by theapplicant for the peptides of the invention.<20% = +; 20%-49% = ++; 50%-69% = +++; >=70% = ++++ Seq Wells positiveID No Sequence [%] HLA   2 TLLKALLEI ++ A*02   3 ALIYNLVGI ++ A*02   4ALFKAWAL ++++ A*02   5 RLLDFINVL ++ A*02   7 ALQAFEFRV ++++ A*02  60GLLSLTSTLYL + A*02  62 KVLGVNVML ++ A*02  64 FLDPDRHFL +++ A*02  66GLLQELSSI + A*02  67 SLLLPSIFL +++ A*02  71 YLEDTDRNL + A*02  73FLIEELLFA +++ A*02  75 KVVSVLYNV +++ A*02  11 SYSDLHYGF +++ A*24  12KYEKIFEML + A*24  13 VYTFLSSTL + A*24  16 IYSPQFSRL + A*24  18KYPVHIYRL + A*24  79 SYNEHWNYL + A*24  80 TAYMVSVAAF + A*24  82SYFRGFTLI + A*24 113 QLDSNRLTY + A*01 115 FVDNQYWRY + A*01  20RMASPVNVK + A*03  21 AVRKPIVLK + A*03  22 SLKERNPLK + A*03  23 GMMKGGIRK++ A*03  24 SMYYPLQLK + A*03  25 GTSPPSVEK +++ A*03  26 RISEYLLEK + A*03 27 VLYGPAGLGK + A*03  28 KTYETNLEIKK + A*03  30 ALEVAHRLK ++ A*03  83GTYAHTVNR + A*03  84 KLQPAQTAAK + A*03  85 VLLGSLFSRK + A*03  86VVLLGSLFSRK + A*03  87 AVAPPTPASK + A*03  90 KVAGERYVYK +++ A*03  91RSLRYYYEK ++ A*03  94 ATFERVLLR + A*03  95 QSMYYPLQLK + A*03  99KVVDRWNEK ++ A*03 100 RLFTSPIMTK + A*03 102 SVLTSSLVK + A*03 106AAFVPLLLK +++ A*03 109 KTFTIKRFLAK + A*03 110 SAAPPSYFR ++ A*03  32SPNKGTLSV + B*07  33 SPTFHLTL ++++ B*07  34 LPRGPLASLL + B*07  35FPDNQRPAL + B*07  36 APAAWLRSA +++ B*07  37 RPLFQKSSM + B*07  38SPHPVTALLTL + B*07  39 RPAPFEVVF +++ B*07  40 KPGTSYRVTL ++++ B*07  41RVRSRISNL + B*07 118 SPASRSISL + B*07 119 APLPRPGAVL ++ B*07 120RPAMNYDKL + B*07 121 VPNQSSESL + B*07 123 KPSESIYSAL ++ B*07 124LPSDSHFKITF ++ B*07 128 YPRTITPGM + B*07 129 APRPASSL + B*07 130FPRLVGPDF +++ B*07 131 APTEDLKAL ++ B*07 133 MPNLPSTTSL ++++ B*07 134RPIVPGPLL ++ B*07 139 SPQSMSNTL + B*07 140 SPRTEASSAVL + B*07 141SPMTSLLTSGL ++ B*07 146 IPRPEVQAL +++ B*07 147 APRWFPQPTVV ++ B*07 148KPYGGSGPL + B*07 149 GPREALSRL ++ B*07  52 AEFLLRIFL + B*44  53MEHPGKLLF + B*44  55 HETETRTTW +++ B*44  57 QESDLRLFL + B*44  58GEMEQKQL ++++ B*44  59 SENVTMKVV ++ B*44 174 AEATARLNVF + B*44 175AEIEPKADG ++++ B*44 177 TEVGTMNLF ++ B*44 178 NELFRDGVNW + B*44 179REAGDEFEL + B*44 180 REAGDEFELRY ++++ B*44 181 GEGPKTSW + B*44 182KEATEAQSL + B*44 183 YEKGIMQKV ++++ B*44 184 AELEALTDLW + B*44 186REGPEEPGL + B*44 187 GEAQTRIAW ++ B*44 188 AEFAKKQPWW ++ B*44 189KEFLFNMY ++++ B*44 190 YEVARILNL ++++ B*44 191 EEDAALFKAW +++ B*44 192YEFKFPNRL + B*44 195 AEDKRHYSV +++ B*44 197 AEVLLPRLV ++ B*44 198QEAARAAL ++ B*44 199 REIDESLIFY + B*44 200 AESIPTVSF +++ B*44 201AETILTFHAF +++ B*44 202 HESEATASW ++ B*44 203 IEHSTQAQDTL ++++ B*44 205SEITRIEM ++++ B*44 207 TEARATSDSW + B*44 208 TEVSRTEAI + B*44 209TEVSRTEL ++++ B*44 210 VEAADIFQNF + B*44 211 EEKVFPSPLW +++ B*44 212MEQKQLQKRF ++ B*44 213 KESIPRWYY + B*44

Example 4

Synthesis of Peptides

All peptides were synthesized using standard and well-established solidphase peptide synthesis using the Fmoc-strategy. Identity and purity ofeach individual peptide have been determined by mass spectrometry andanalytical RP-HPLC. The peptides were obtained as white to off-whitelyophilizes (trifluoro acetate salt) in purities of >50%. All TUMAPs arepreferably administered as trifluoro-acetate salts or acetate salts,other salt-forms are also possible.

Example 5

MHC Binding Assays

Candidate peptides for T cell based therapies according to the presentinvention were further tested for their MHC binding capacity (affinity).The individual peptide-MHC complexes were produced by UV-ligandexchange, where a UV-sensitive peptide is cleaved upon UV-irradiation,and exchanged with the peptide of interest as analyzed. Only peptidecandidates that can effectively bind and stabilize the peptide-receptiveMHC molecules prevent dissociation of the MHC complexes. To determinethe yield of the exchange reaction, an ELISA was performed based on thedetection of the light chain (β2m) of stabilized MHC complexes. Theassay was performed as generally described in Rodenko et al. (Rodenko etal., 2006).

96 well MAXISorp plates (NUNC) were coated over night with 2 ug/mlstreptavidin in PBS at room temperature, washed 4× and blocked for 1 hat 37° C. in 2% BSA containing blocking buffer. RefoldedHLA-A*02:01/MLA-001 monomers served as standards, covering the range of15-500 ng/ml. Peptide-MHC monomers of the UV-exchange reaction werediluted 100-fold in blocking buffer. Samples were incubated for 1 h at37° C., washed four times, incubated with 2 ug/ml HRP conjugatedanti-β2m for 1 h at 37° C., washed again and detected with TMB solutionthat is stopped with NH₂SO₄. Absorption was measured at 450 nm.Candidate peptides that show a high exchange yield (preferably higherthan 50%, most preferred higher than 75%) are generally preferred for ageneration and production of antibodies or fragments thereof, and/or Tcell receptors or fragments thereof, as they show sufficient avidity tothe MHC molecules and prevent dissociation of the MHC complexes.

TABLE 12  MHC class I binding scores. Binding ofHLA-class I restricted peptides to HLA-A*02:01 was ranged by peptide exchange yield: >10% = +; >20% = ++; >50 = +++; >75% = ++++Peptide Seq ID No Sequence exchange   1 MIPTFTALL +++   2 TLLKALLEI ++++  3 ALIYNLVGI ++++   4 ALFKAWAL ++++   5 RLLDFINVL ++++   6 SLGKHTVAL+++   7 ALQAFEFRV ++++   8 YLVTKVVAV ++++   9 VLLAGFKPPL +  60GLLSLTSTLYL ++++  61 YMVHIQVTL ++++  62 KVLGVNVML ++++  63 MMEEMIFNL++++  64 FLDPDRHFL ++++  66 GLLQELSSI ++++  67 SLLLPSIFL ++++  68KLFDTQQFL ++++  69 TTYEGSITV ++++  70 VLQGLLRSL ++++  71 YLEDTDRNL ++++ 72 YLTDLQVSL ++++  73 FLIEELLFA ++++  75 KVVSVLYNV ++++ 216 IMFDDAIERA++++ 217 VSSSLTLKV + 219 PLPRPGAVL + 220 RMTTQLLLL +++ 221 SLLDLYQL ++222 ALMRLIGCPL ++++ 223 FAHHGRSL + 224 SLPRFQVTL ++++ 225 SVFAHPRKL +++227 YTFRYPLSL +++ 228 RLWDWVPLA ++++ 229 ISVPAKTSL + 231 SVTESTHHL +++232 TISSLTHEL ++++ 234 GVATRVDAI ++ 236 SAIPFSMTL +++ 241 RQPNILVHL ++242 STIPALHEI +++ 243 YASEGVKQV +++ 244 DTDSSVHVQV +

TABLE 13  MHC class I binding scores. Bindingof HLA-class I restricted peptides to HLA-A*24:02 was ranged by peptide exchange yield: >10% = +; >20% = ++; >50 = +++; >75% = ++++Peptide Seq ID No Sequence exchange  10 RYSDSVGRVSF ++++  11 SYSDLHYGF++++  12 KYEKIFEML ++++  13 VYTFLSSTL ++++  14 FYFPTPTVL ++++  15VYHDDKQPTF ++++  16 IYSPQFSRL ++++  17 RFTTMLSTF ++++  18 KYPVHIYRL ++++ 19 KYVKVFHQF ++++  76 KYVAELSLL ++++  77 RYGPVFTV ++++  78 SFAPRSAVF++++  79 SYNEHWNYL ++++  80 TAYMVSVAAF +++  81 VYNHTTRPL ++++  82SYFRGFTLI ++++ 246 RYLAVVHAVF ++++ 249 VYTPTLGTL ++++ 252 LYQPRASEM +++255 VFVSFSSLF +++

TABLE 14  MHC class I binding scores. Bindingof HLA-class I restricted peptides to HLA-A*01:01 was ranged by peptide exchange yield: >10% = +; >20% = ++; >50 = +++; >75% = ++++Peptide Seq ID No Sequence exchange  31 LLDEGAMLLY ++++ 112 TVTGAEQIQY++ 113 QLDSNRLTY +++ 114 VMEQSAGIMY ++ 115 FVDNQYWRY +++ 116 VLLDEGAMLLY++ 288 SPVTSVHGGTY ++ 289 RWEKTDLTY ++ 290 DMDEEIEAEY ++ 291 ETIRSVGYY+++ 292 NVTMKVVSVLY +++

TABLE 15  MHC class I binding scores. Binding ofHLA-class I restricted peptides to HLA-A*03:01 was ranged by peptide exchange yield: >10% = +; >20% = ++; >50 = +++; >75% = ++++Peptide Seq ID No Sequence exchange  20 RMASPVNVK ++++  21 AVRKPIVLK +++ 22 SLKERNPLK ++  23 GMMKGGIRK +++  24 SMYYPLQLK +++  25 GTSPPSVEK ++ 26 RISEYLLEK ++  27 VLYGPAGLGK +++  28 KTYETNLEIKK +++  30 ALEVAHRLK ++ 83 GTYAHTVNR +++  84 KLQPAQTAAK ++  85 VLLGSLFSRK ++  86 VVLLGSLFSRK ++ 87 AVAPPTPASK ++  88 VVHAVFALK +++  89 RVAELLLLH ++  90 KVAGERYVYK +++ 91 RSLRYYYEK ++  93 KILEEHTNK ++  94 ATFERVLLR +++  95 QSMYYPLQLK ++ 98 LLQPPPLLAR ++  99 KVVDRWNEK ++ 100 RLFTSPIMTK +++ 101 RVFTSSIKTK ++102 SVLTSSLVK ++ 104 VLADSVTTK ++ 105 RLFSWLVNR +++ 106 AAFVPLLLK ++ 107RLQEWKALK +++ 109 KTFTIKRFLAK ++ 110 SAAPPSYFR ++ 256 RTEEVLLTFK ++ 257VTADHSHVF + 258 GAYAHTVNR +++ 259 KTLELRVAY ++ 260 GTNTVILEY +++ 261HTFGLFYQR ++ 262 RSRLNPLVQR ++ 263 SSSSATISK ++ 264 AIKVIPTVFK ++ 265QIHDHVNPK ++ 266 ISYSGQFLVK +++ 267 VTDLISPRK ++ 269 RLKGDAWVYK +++ 270AVFNPRFYRTY ++ 271 RMFADDLHNLNK +++ 272 RQPERTILRPR ++ 273 RVNAIPFTY +++274 KTFPASTVF + 275 STTFPTLTK ++ 276 VSKTTGMEF + 277 TTALKTTSR + 278NLSSITHER ++ 279 SVSSETTKIKR ++ 280 SVSGVKTTF ++ 281 RAKELEATF + 283IVQEPTEEK ++ 284 KSLIKSWKK ++ 285 GTVNPTVGK ++ 286 TVAPPQGVVK ++ 287RRIHTGEKPYK ++

TABLE 16  MHC class I binding scores. Binding ofHLA-class I restricted peptides to HLA-B*07:02 was ranged by peptide exchange yield:  >10% = +; >20% = 30 +; >50 = +++; >75% = ++++Peptide Seq ID No Sequence exchange  32 SPNKGTLSV ″+++″  33 SPTFHLTL″+++″  34 LPRGPLASLL ″+++″  35 FPDNQRPAL ″+++″  36 APAAWLRSA ″++″  37RPLFQKSSM ″+++″  38 SPHPVTALLTL ″+++″  39 RPAPFEVVF ″+++″  40 KPGTSYRVTL″+++″  41 RVRSRISNL ″+++″ 118 SPASRSISL ″+++″ 119 APLPRPGAVL ″+++″ 120RPAMNYDKL ″++″ 121 VPNQSSESL ″+++″ 122 YPGFPQSQY ″++″ 123 KPSESIYSAL″+++″ 124 LPSDSHFKITF ″+++″ 125 VPVYILLDEM ″++″ 126 KPGPEDKL ″++″ 127APRAGSQVV ″+++″ 128 YPRTITPGM ″+++″ 129 APRPASSL ″+++″ 130 FPRLVGPDF″+++″ 131 APTEDLKAL ″+++″ 132 IPGPAQSTI ″++″ 133 MPNLPSTTSL ″+++″ 134RPIVPGPLL ″+++″ 135 RVRSTISSL ″+++″ 136 SPFSAEEANSL ″+++″ 137 SPGATSRGTL″+++″ 138 SPMATTSTL ″+++″ 139 SPQSMSNTL ″+++″ 140 SPRTEASSAVL ″+++″ 141SPMTSLLTSGL ″+++″ 142 TPGLRETSI ″++″ 143 SPAMTSTSF ″++″ 144 SPSPVSSTL″+++″ 145 SPSSPMSTF ″++″ 146 IPRPEVQAL ″+++″ 147 APRWFPQPTVV ″+++″ 148KPYGGSGPL ″+++″ 149 GPREALSRL ″+++″ 293 VPDSGATATAY ″++″ 294 YPLRGSSIF″+++″ 295 YPLRGSSIFGL ″+++″ 296 YPLRGSSI ″++″ 297 TVREASGLL ″+++″ 298YPTEHVQF ″++″ 299 HPGSSALHY ″++″ 300 IPMAAVKQAL ″+++″ 301 SPRRSPRISF″++″ 302 RVEEVRALL ″+++″ 303 LPMWKVTAF ″+++″ 304 LPRPGAVL ″+++″ 305TPWAESSTKF ″++″ 306 APVIFSHSA ″++″ 307 LPYGPGSEAAAF ″+++″ 308 YPEGAAYEF″++″ 309 FPQSQYPQY ″++++″ 311 RPLFYVVSL ″++″ 312 LPYFREFSM ″+++″ 313KVKSDRSVF ″+″ 314 VPDQPHPEI ″+++″ 315 SPRENFPDTL ″+++″ 316 EPKTATVL ″++″317 FPFQPGSV ″+++″ 318 FPNRLNLEA ″+++″ 319 SPAEPSVYATL ″++++″ 320FPMSPVTSV ″+++″ 321 SPMDTFLLI ″++″ 322 SPDPSKHLL ″++″ 323 RPMPNLRSV″+++″ 324 VPYRVVGL ″++″ 325 GPRNAQRVL ″+++″ 326 VPSEIDAAF ″++″ 327SPLPVTSLI ″+++″ 328 EPVTSSLPNF ″++″ 329 FPAMTESGGMIL ″+++″ 330FPFVTGSTEM ″++″ 331 FPHPEMTTSM ″+++″ 332 FPHSEMTTL ″+++″ 333 FPHSEMTTVM″+++″ 334 FPYSEVTTL ″+++″ 335 HPDPVGPGL ″++″ 336 HPKTESATPAAY ″++″ 337HPVETSSAL ″+++″ 338 HVTKTQATF ″++″ 339 LPAGTTGSLVF ″+++″ 340 LPEISTRTM″++″ 341 LPLDTSTTL ″+++″ 342 LPLGTSMTF ″+++″ 343 LPSVSGVKTTF ″++″ 344LPTQTTSSL ″+++″ 345 LPTSESLVSF ″++″ 346 LPWDTSTTLF ″+++″ 347 MPLTTGSQGM″++″ 348 MPNSAIPFSM ″+++″ 349 MPSLSEAMTSF ″+++″ 350 NPSSTTTEF ″+++″ 351NVLTSTPAF ″++″ 352 SPAETSTNM ″+++″ 353 SPAMTTPSL ″+++″ 354 SPLPVTSLL″+++″ 355 SPLVTSHIM ″+++″ 356 SPNEFYFTV ″+++″ 357 SPSPVPTTL ″+++″ 358SPSPVTSTL ″+++″ 359 SPSTIKLTM ″+++″ 360 SPSVSSNTY ″++″ 361 SPTHVTQSL″+++″ 362 SPVPVTSLF ″+++″ 363 TAKTPDATF ″++″ 364 TPLATTQRF ″++″ 365TPLATTQRFTY ″++″ 367 TPSVVTEGF ″++″ 368 VPTPVFPTM ″++″ 369 FPHSEMTTV″+++″ 370 PGGTRQSL ″+″ 371 LYVDGFTHW ″++″ 372 IPRNPPPTLL ″+++″ 373RPRALRDLRIL ″+++″ 374 NPIGDTGVKF ″+++″ 375 AAASPLLLL ″++″ 376 RPRSPAGQVA″+++″ 377 RPRSPAGQVAAA ″+++″ 378 RPRSPAGQVAA ″+++″ 379 GPFPLVYVL ″+++″380 IPTYGRTF ″+++″ 381 LPEQTPLAF ″++″ 382 SPMHDRWTF ″+++″ 383 TPTKETVSL″+++″ 384 YPGLRGSPM ″++++″ 385 SPALHIGSV ″+++″ 386 FPFNPLDF ″++″ 387APLKLSRTPA ″+++″ 388 SPAPLKLSRTPA ″++″ 389 SPGAQRTFFQL ″+++″ 390NPDLRRNVL ″+++″ 391 APSTPRITTF ″+++″ 392 KPIESTLVA ″+++″

TABLE 17  MHC class I binding scores. Binding of HLA-class I restricted peptides to HLA-B*44:02 was measured by peptide exchange yield: >10% = +; >20% = ++; >50 =+++; >75% = ++++Peptide Seq ID No Sequence exchange  52 AEFLLRIFL ″++″  53 MEHPGKLLF″++++″  54 AEITITTQTGY ″+++″  55 HETETRTTW ″+++″  56 SEPDTTASW ″+++″  57QESDLRLFL ″+++″  58 GEMEQKQL ″++″  59 SENVTMKVV ″+++″ 173 AEAQVGDERDY″+++″ 174 AEATARLNVF ″++++″ 175 AEIEPKADG ″++″ 176 AEIEPKADGSW ″+++″ 177TEVGTMNLF ″+++″ 178 NELFRDGVNW ″+++″ 179 REAGDEFEL ″++″ 180 REAGDEFELRY″++″ 181 GEGPKTSW ″++″ 182 KEATEAQSL ″+++″ 183 YEKGIMQKV ″++″ 184AELEALTDLW ″+++″ 185 AERQPGAASL ″++″ 186 REGPEEPGL ″++″ 187 GEAQTRIAW″+++″ 188 AEFAKKQPWW ″+++″ 189 KEFLFNMY ″++″ 190 YEVARILNL ″++″ 191EEDAALFKAW ″+++″ 192 YEFKFPNRL ″+++″ 193 LEAQQEAL ″++″ 194 KEVDPTSHSY″++″ 195 AEDKRHYSV ″++″ 196 REMPGGPVW ″+++″ 197 AEVLLPRLV ″+++″ 198QEAARAAL ″++″ 199 REIDESLIFY ″+++″ 200 AESIPTVSF ″+++″ 201 AETILTFHAF″+++″ 202 HESEATASW ″+++″ 203 IEHSTQAQDTL ″++″ 204 RETSTSEETSL ″+++″ 205SEITRIEM ″++″ 206 SESVTSRTSY ″+++″ 207 TEARATSDSW ″+++″ 208 TEVSRTEAI″++″ 209 TEVSRTEL ″++″ 210 VEAADIFQNF ″+++″ 211 EEKVFPSPLW ″+++″ 212MEQKQLQKRF ″+++″ 213 KESIPRWYY ″++″ 214 VEQTRAGSLL ″++″ 215 SEDGLPEGIHL″++″ 396 REASGLLSL ″+++″ 397 REGDTVQLL ″++″ 398 SFEQVVNELF ″++″ 399RELLHLVTL ″+++″ 400 GEIEIHLL ″+″ 402 RELANDELIL ″++″ 403 EEAQWVRKY ″++″404 NEAIMHQY ″++″ 405 NEIWTHSY ″+″ 406 EDGRLVIEF ″+″ 407 AEHEGVSVL ″++″408 LEKALQVF ″++″ 409 REFVLSKGDAGL ″+++″ 410 SEDPSKLEA ″+″ 411 LELPPILVY″+″ 412 QEILTQVKQ ″++″ 413 IEALSGKIEL ″++″ 414 EDAALFKAW ″++″ 415REEDAALFKAW ″+++″ 416 SEEETRVVF ″+++″ 417 AEHFSMIRA ″++″ 418 FEDAQGHIW″+++″ 419 HEFGHVLGL ″++″ 420 FESHSTVSA ″+″ 421 GEPATTVSL ″++″ 422SETTFSLIF ″+++″ 423 SEVPTGTTA ″++″ 424 TEFPLFSAA ″+″ 425 SEVPLPMAI ″+++″426 PEKTTHSF ″+″ 427 HESSSHHDL ″++″ 429 REKFIASVI ″++″ 431 AEQDPDELNKA″++″ 432 EEQYIAQF ″+″ 433 SDSQVRAF ″+″ 434 KEAIREHQM ″++″ 435 REEFVSIDHL″++″ 436 REPGDIFSEL ″++″ 437 TEAVVTNEL ″++″ 438 SEVDSPNVL ″+++″

Example 6

Stability of Peptide-MHC Class I Complexes

Peptide-MHC stability assays for HLA-B*08:01 peptides were performed.The data were obtained using a proximity based, homogenous, real-timeassay in order to measure the dissociation of peptides from HLA class Imolecules. First, human recombinant HLA-B*08:01 and b2m were expressedin E. coli and purified in a series of liquid chromatography based steps(Ferre et al., 2003; Ostergaard et al., 2001). Then, the stability of apeptide-MHC complex (pMHC) was determined by measuring the amount of b2massociated with the MHC heavy chain over time at 37° C. (Harndahl etal., 2012). The stability of each pMHC, expressed as the half life ofb2m associated with the respective heavy chain, was calculated byfitting the data to a one-phase dissociation equation.

The pMHC stabilities were measured in three independent experiments withthe peptides in question, and for HLA-B*08:01 were found to span therange from weak-binders (+) to very stable binders (++++). The meanhalf-life (T1/2) is shown in Table 18.

TABLE 18  Mean half-life (T1/2) based on three individualmeasurements. T1/2 > 2 h = +; T1/2 > 4 h = ++; T1/2 > 6 h = +++; T1/2 > 10 h = ++++ Mean Half-life Seq ID No Sequence(T1/2)  43 ALKARTVTF +++  44 LNKQKVTF ++++  45 VGREKKLAL ++  46DMKKAKEQL +  47 MPNLRSVDL ++  48 DVKKKIKEV +  49 LPRLKAFMI ++  50DMKYKNRV +  51 SLRLKNVQL + 150 MAAVKQAL ++ 151 HLLLKVLAF ++ 152MGSARVAEL ++ 153 NAMLRKVAV + 154 MLRKIAVAA + 156 HVKEKFLL ++ 157EAMKRLSYI + 158 LPKLAGLL + 159 VLKHKLDEL + 160 YPKARLAF +++ 161ALKTTTTAL + 162 QAKTHSTL + 163 QGLLRPVF ++ 164 SIKTKSAEM +++ 166TPKLRETSI ++ 167 TSHERLTTL ++ 169 TSMPRSSAM +++ 170 YLLEKSRVI ++ 171FAFRKEAL ++ 172 KLKERNREL +++ 394 MYKMKKPI + 395 VLLPRLVSC +

Example 7

Binding Scores of Selected Peptides for HLA Class II Allotypes

Major histocompatibility complex class II (MHC-II) molecules arepredominantly expressed on the surface of professional antigenpresenting cells, where they display peptides to T helper cells, whichorchestrate the onset and outcome of many host immune responses.Understanding which peptides will be presented by the MHC-II molecule istherefore important for understanding the activation of T helper cellsand can be used to identify T-cell epitopes. Peptides presented by theMHC class II molecule bind to a binding groove formed by residues of theMHC α- and β-chain. The peptide-MHC binding affinity is primarilydetermined by the amino acid sequence of the peptide-binding core. HLAclass II binding prediction algorithms are only available for the mostimportant class II alleles and have been tested using the SYFPEITHIalgorithm (Rammensee et al., 1999). The algorithm has already beensuccessfully used to identify class I and class II epitopes from a widerange of antigens, e.g. from the human tumor-associated antigens TRP2(class I) (Sun et al., 2000) and SSX2 (class II) (Neumann et al., 2004).Table 20 shows the HLA class II allotypes which are likely to bind theselected peptides. The peptide was considered as binding to an HLAmolecule if the SYFPEITHI score was equal to or higher than 18.

TABLE 20Binding of the class II peptides to various HLA class II allotypes. Based on the prediction by the SYFPEITHI algorithm, the selected peptides are likely to bind to at least 4 of the HLA class II allotypes with known binding motif. Listed are all HLA class IIalleles for which a SYFPEITHI prediction matrix is available. SeqNo of HLA ID Best HLA class II Class II No Sequence bindersHLA Class II binders binder 552 GVNAMLRKVAVAAASKPH DRB1*11:04DQA1*05:01/DQB1*02:01 (DQ2), 15 VE QA1*05:01/DQB1*03:01 (DQ7),DQB1*06:02, DRB1*01:01, DRB1*04:01, DRB1*04:02, DRB1*04:04, DRB1*04:05,DRB1*07:01, DRB1*09:01, DRB1*11:01, DRB1*11:04, DRB1*13:01, DRB1*13:02,DRB1*15:01 560 PNFSGNWKIIRSENFEELL DRB1*07:01DQA1*05:01/DQB1*02:01 (DQ2), 14 K DRB1*01:01, DRB1*03:01, DRB1*04:01,DRB1*04:04, DRB1*04:05, DRB1*07:01, DRB1*08:02, DRB1*08:03, DRB1*09:01,DRB1*11:01, DRB1*13:02, DRB1*15:01, DRB1*15:02 574 LPDFYNDWMFIAKHLPDLDRB1*11:01 DQA1*05:01/DQB1*02:01 (DQ2), 15DRB1*01:01, DRB1*03:01, DRB1*04:01, DRB1*04:02, DRB1*04:04, DRB1*04:05,DRB1*07:01, DRB1*08:02, DRB1*08:03, DRB1*11:01, DRB1*11:04, DRB1*13:02,DRB1*15:01, DRB1*15:02 575 VGDDHLLLLQGEQLRRT DRB1*01:01DQA1*05:01/DQB1*02:01 (DQ2),  8 DRB1*01:01, DRB1*03:01, DRB1*04:01,DRB1*04:04, DRB1*09:01, DRB1*15:01, DRB1*15:02 579 SGGPLVCDETLQGILSDQA1*0501/DQB1*0201  DQA1*05:01/DQB1*02:01 (DQ2),  8 (DQ2)DQA1*05:01/DQB1*03:01 (DQ7), DRB1*01:01, DRB1*03:01, DRB1*04:01,DRB1*04:04, DRB1*04:05, DRB1*15:01 582 GSQPWQVSLFNGLSFH DRB1*15:01DQA1*05:01/DQB1*02:01 (DQ2), 10 DQB1*06:02, DRB1*01:01, DRB1*03:01,DRB1*04:01, DRB1*04:04, DRB1*07:01, DRB1*09:01, DRB1*15:01, DRB1*15:02583 LTVKLPDGYEFKFPNRLNL DQA1*05:01/DQB1*02:01 DQA1*05:01/DQB1*02:01 (DQ2), 14 EAINY (DQ2)DRB1*01:01, DRB1*03:01, DRB1*04:01, DRB1*04:04, DRB1*04:05, DRB1*07:01,DRB1*08:02, DRB1*08:03, DRB1*09:01, DRB1*11:01, DRB1*13:02, DRB1*15:01,DRB1*15:02 587 DQANLTVKLPDGYEFKFP DQA1*05:01/DQB1*02:01 DQA1*05:01/DQB1*02:01 (DQ2), 13 NRLNL (DQ2)DRB1*01:01, DRB1*03:01, DRB1*04:01, DRB1*04:04, DRB1*04:05, DRB1*07:01,DRB1*08:02, DRB1*08:03, DRB1*11:01, DRB1*13:02, DRB1*15:01, DRB1*15:02588 VAPDAKSFVLNLGKDSNN DRB1*01:01 DQA1*05:01/DQB1*02:01 (DQ2), 16 LDQA1*05:01/DQB1*03:01 (DQ7), DRB1*01:01, DRB1*03:01, DRB1*04:01,DRB1*04:02, DRB1*04:04, DRB1*04:05, DRB1*07:01, DRB1*08:02, DRB1*08:03,DRB1*09:01, DRB1*11:01, DRB1*11:04, DRB1*13:01, DRB1*13:02 590RVRGEVAPDAKSFVLNLG DRB1*03:01 DQA1*05:01/DQB1*02:01 (DQ2), 10DQA1*05:01/DQB1*03:01 (DQ7), DRB1*01:01, DRB1*03:01, DRB1*04:01,DRB1*04:04, DRB1*07:01, DRB1*09:01, DRB1*11:04, DRB1*15:01 596MAADGDFKIKCVAFD DQA1*05:01/DQB1*02:01  DQA1*05:01/DQB1*02:01 (DQ2), 10(DQ2); DRB1*03:01; DRB1*01:01, DRB1*03:01, DRB1*04:01, DRB1*07:01DRB1*04:04, DRB1*04:05, DRB1*07:01, DRB1*08:03, DRB1*09:01, DRB1*15:01597 SPDAESLFREALSNKVDEL DRB1*07:01 DQA1*05:01/DQB1*02:01 (DQ2),  8DQA1*05:01/DQB1*03:01 (DQ7), DRB1*01:01, DRB1*04:01, DRB1*04:04,DRB1*04:05, DRB1*07:01, DRB1*09:01 601 LSNKVDELAHFLLRKDQA1*05:01/DQB1*02:01  DQA1*05:01/DQB1*02:01 (DQ2), 14 (DQ2)DRB1*01:01, DRB1*03:01, DRB1*04:01, DRB1*04:02, DRB1*04:04, DRB1*04:05,DRB1*07:01, DRB1*08:02, DRB1*08:03, DRB1*11:01, DRB1*11:04, DRB1*15:01,DRB1*15:02 604 KLITQDLVKLKYLEYRQ DQA1*05:01/DQB1*02:01 DQA1*05:01/DQB1*02:01 (DQ2),  9 (DQ2)DRB1*01:01, DRB1*03:01, DRB1*04:01, DRB1*04:04, DRB1*08:02, DRB1*13:01,DRB1*13:02, DRB1*15:01 605 LTVAEVQKLLGPHVEGLKA DRB1*01:01DQA1*05:01/DQB1*02:01 (DQ2), 15 EERHRP DQA1*05:01/DQB1*03:01 (DQ7),DRB1*01:01, DRB1*03:01, DRB1*04:01, DRB1*04:02, DRB1*04:04, DRB1*04:05,DRB1*07:01, DRB1*09:01, DRB1*11:01, DRB1*11:04, DRB1*13:01, DRB1*15:01,DRB1*15:02 622 MDALRGLLPVLGQPIIRSIP DRB1*01:01DQA1*05:01/DQB1*02:01 (DQ2), 15 QGIVA DQA1*05:01/DQB1*03:01 (DQ7),DQB1*06:02, DRB1*01:01, DRB1*03:01, DRB1*04:01, DRB1*04:02, DRB1*04:04,DRB1*04:05, DRB1*07:01, DRB1*09:01, DRB1*11:01, DRB1*11:04, DRB1*15:01,DRB1*15:02 645 RGLLPVLGQPIIRSIPQGIV DRB1*01:01;DQA1*05:01/DQB1*02:01 (DQ2), 14 AAWRQ DRB1*09:01DQA1*05:01/DQB1*03:01 (DQ7), DQB1*06:02, DRB1*01:01, DRB1*03:01,DRB1*04:01, DRB1*04:02, DRB1*04:04, DRB1*07:01, DRB1*09:01, DRB1*11:01,DRB1*11:04, DRB1*15:01, DRB1*15:02 658 VSTMDALRGLLPVLGQPII DRB1*01:01DQA1*05:01/DQB1*02:01 (DQ2), 14 RSIPQG DQA1*05:01/DQB1*03:01 (DQ7),DQB1*06:02, DRB1*01:01, DRB1*03:01, DRB1*04:01, DRB1*04:02, DRB1*04:04,DRB1*04:05, DRB1*09:01, DRB1*11:01, DRB1*11:04, DRB1*15:01, DRB1*15:02662 LRTDAVLPLTVAEVQKLLG DRB1*01:01 DQA1*05:01/DQB1*02:01 (DQ2), 15 PHVEGDQA1*05:01/DQB1*03:01 (DQ7), DRB1*01:01, DRB1*03:01, DRB1*04:01,DRB1*04:02, DRB1*04:04, DRB1*04:05, DRB1*07:01, DRB1*09:01, DRB1*11:01,DRB1*11:04, DRB1*13:01, DRB1*15:01, DRB1*15:02 669 VLPLTVAEVQKLLGPHVEGDRB1*01:01 DQA1*05:01/DQB1*02:01 (DQ2), 15 LKAEEDQA1*05:01/DQB1*03:01 (DQ7), DRB1*01:01, DRB1*03:01, DRB1*04:01,DRB1*04:02, DRB1*04:04, DRB1*04:05, DRB1*07:01, DRB1*09:01, DRB1*11:01,DRB1*11:04, DRB1*13:01, DRB1*15:01, DRB1*15:02 672 LRGLLPVLGQPIIRSIPQGIDRB1*01:01 DQA1*05:01/DQB1*02:01 (DQ2), 14 VAADQA1*05:01/DQB1*03:01 (DQ7), DQB1*06:02, DRB1*01:01, DRB1*03:01,DRB1*04:01, DRB1*04:02, DRB1*04:04,, DRB1*07:01, DRB1*09:01, DRB1*11:01,DRB1*11:04, DRB1*15:01, DRB1*15:02 673 IPFTYEQLDVLKHKLDELY DRB1*08:03DQA1*05:01/DQB1*02:01 (DQ2), 15 PQ DRB1*01:01, DRB1*03:01, DRB1*04:01,DRB1*04:04, DRB1*04:05, DRB1*07:01, DRB1*08:02, DRB1*08:03, DRB1*09:01,DRB1*11:01, DRB1*11:04, DRB1*13:02, DRB1*15:01, DRB1*15:02 676VPPSSIWAVRPQDLDTCD DQA1*05:01/DQB1*02:01  DQA1*05:01/DQB1*02:01 (DQ2),10 PR (DQ2) DRB1*01:01, DRB1*03:01, DRB1*04:01,DRB1*04:04, DRB1*04:05, DRB1*07:01, DRB1*08:03, DRB1*09:01, DRB1*15:01679 WGVRGSLLSEADVRALGG DRB1*09:01 DQA1*05:01/DQB1*02:01 (DQ2), 12 LADQA1*05:01/DQB1*03:01 (DQ7), DRB1*01:01, DRB1*03:01, DRB1*04:01,DRB1*04:02, DRB1*04:04, DRB1*04:05, DRB1*07:01, DRB1*09:01, DRB1*11:01,DRB1*15:01 706 LSTERVRELAVALAQKNVK DQA1*05:01/DQB1*03:01 DQA1*05:01/DQB1*02:01 (DQ2), 15 (DQ7) DQA1*05:01/DQB1*03:01 (DQ7),DQB1*06:02, DRB1*01:01, DRB1*03:01, DRB1*04:01, DRB1*04:02, DRB1*04:04,DRB1*04:05, DRB1*09:01, DRB1*11:01, DRB1*11:04, DRB1*13:01, DRB1*15:01,DRB1*15:02 714 AIPFTYEQLDVLKHKLDE DRB1*08:03DQA1*05:01/DQB1*02:01 (DQ2), 15 DRB1*01:01, DRB1*03:01, DRB1*04:01,DRB1*04:04, DRB1*04:05, DRB1*07:01, DRB1*08:02, DRB1*08:03, DRB1*09:01,DRB1*11:01, DRB1*11:04, DRB1*13:02, DRB1*15:01, DRB1*15:02 715GLSTERVRELAVALAQKN DQA1*05:01/DQB1*03:01  DQA1*05:01/DQB1*02:01 (DQ2),15 (DQ7) DQA1*05:01/DQB1*03:01 (DQ7),DQB1*06:02, DRB1*01:01, DRB1*03:01, DRB1*04:01, DRB1*04:02, DRB1*04:04,DRB1*04:05, DRB1*09:01, DRB1*11:01, DRB1*11:04, DRB1*13:01, DRB1*15:01,DRB1*15:02 717 IPQGIVAAWRQRSSRDPS DRB1*11:04DQA1*05:01/DQB1*02:01 (DQ2), 13 DQA1*05:01/DQB1*03:01 (DQ7),DRB1*01:01, DRB1*03:01, DRB1*04:01, DRB1*04:02, DRB1*04:04, DRB1*04:05,DRB1*07:01, DRB1*11:01, DRB1*11:04, DRB1*13:01, DRB1*15:01 720ALGGLACDLPGRFVAES DQA1*05:01/DQB1*02:01  DQA1*05:01/DQB1*02:01 (DQ2),  8(DQ2) DQA1*05:01/DQB1*03:01 (DQ7), DQB1*06:02, DRB1*01:01, DRB1*03:01,DRB1*04:05, DRB1*11:01, DRB1*11:04 721 RELAVALAQKNVKLSTEDQA1*05:01/DQB1*03:01  DQA1*05:01/DQB1*03:01 (DQ7), 11 (DQ7)DQB1*06:02, DRB1*01:01, DRB1*03:01, DRB1*04:01, DRB1*04:04, DRB1*04:05,DRB1*09:01, DRB1*11:04, DRB1*13:01, DRB1*15:01 722 LKALLEVNKGHEMSPQDQA1*05:01/DQB1*02:01  DQA1*05:01/DQB1*02:01 (DQ2), 13(DQ2); DRB1*01:01; DQB1*06:02, DRB1*01:01, DRB1*03:01, DRB1*04:05;DRB1*04:01, DRB1*04:02, DRB1*04:04, DRB1*08:03;DRB1*04:05, DRB1*08:03, DRB1*11:01, DRB1*11:04DRB1*11:04, DRB1*13:01, DRB1*15:01 723 TFMKLRTDAVLPLTVA DRB1*01:01DQA1*05:01/DQB1*02:01 (DQ2), 13 DRB1*01:01, DRB1*03:01, DRB1*04:01,DRB1*04:04, DRB1*04:05, DRB1*07:01, DRB1*08:02, DRB1*08:03, DRB1*09:01,DRB1*13:02, DRB1*15:01, DRB1*15:02 727 TLGLGLQGGIPNGYLVDQA1*05:01/DQB1*02:01  DQA1*05:01/DQB1*02:01 (DQ2),  9D(DQ2); RB1*01:01; DRB1*01:01, DRB1*03:01, DRB1*04:01, DRB1*15:01DRB1*04:02, DRB1*04:04, DRB1*07:01, DRB1*09:01, DRB1*15:01 728DLPGRFVAESAEVLL DQA1*05:01/DQB1*02:01  DQA1*05:01/DQB1*02:01 (DQ2), 12(DQ2) DQA1*05:01/DQB1*03:01 (DQ7), DQB1*06:02, DRB1*01:01, DRB1*03:01,DRB1*04:01, DRB1*04:04, DRB1*04:05, DRB1*07:01, DRB1*09:01, DRB1*15:01,DRB1*15:02 732 ERHRPVRDWILRQRQ DRB1*15:01 DQA1*05:01/DQB1*02:01 (DQ2), 4 DRB1*04:01, DRB1*04:04, DRB1*15:01 733 SPRQLLGFPCAEVSG DRB1*01:01DQA1*05:01/DQB1*02:01 (DQ2),  8 DQA1*05:01/DQB1*03:01 (DQ7),DQB1*06:02, DRB1*01:01, DRB1*04:01, DRB1*04:04, DRB1*15:01, DRB1*15:02734 SRTLAGETGQEAAPL DRB1*01:01 DQA1*05:01/DQB1*02:01 (DQ2),  6DRB1*01:01, DRB1*04:01, DRB1*04:04, DRB1*04:05, DRB1*15:01 735VTSLETLKALLEVNK DRB1*01:01 DQA1*05:01/DQB1*02:01 (DQ2), 15DQA1*05:01/DQB1*03:01 (DQ7), DRB1*01:01, DRB1*03:01, DRB1*04:01,DRB1*04:02, DRB1*04:04, DRB1*04:05, DRB1*07:01, DRB1*08:03, DRB1*11:01,DRB1*11:04, DRB1*13:01, DRB1*15:01, DRB1*15:02 745 WELSQLTNSVTELGPYTLDQA1*05:01/DQB1*02:01  DQA1*05:01/DQB1*02:01 (DQ2), 13 DRD(DQ2); DRB1*01:01 DQA1*05:01/DQB1*03:01 (DQ7),DRB1*01:01, DRB1*03:01, DRB1*04:01, DRB1*04:02, DRB1*04:04, DRB1*04:05,DRB1*07:01, DRB1*09:01, DRB1*13:01, DRB1*15:01, DRB1*15:02 746EITITTQTGYSLATSQVTLP DRB1*01:01 DQA1*05:01/DQB1*02:01 (DQ2), 10DQA1*05:01/DQB1*03:01 (DQ7), DRB1*01:01, DRB1*03:01, DRB1*04:01,DRB1*04:04, DRB1*04:05, DRB1*07:01, DRB1*09:01, DRB1*15:01 747ATTPSWVETHSIVIQGFPH DRB1*07:01 DQA1*05:01/DQB1*02:01 (DQ2),  9DQA1*05:01/DQB1*03:01 (DQ7), DRB1*01:01, DRB1*04:01, DRB1*04:04,DRB1*04:05, DRB1*07:01, DRB1*15:01, DRB1*15:02 748 GIKELGPYTLDRNSLYVNGDQA1*05:01/DQB1*02:01  DQA1*05:01/DQB1*02:01 (DQ2), 13 (DQ2); DRB1*01:01DRB1*01:01, DRB1*03:01, DRB1*04:01, DRB1*04:02, DRB1*04:04, DRB1*04:05,DRB1*07:01, DRB1*08:02, DRB1*09:01, DRB1*13:02, DRB1*15:01, DRB1*15:02755 IELGPYLLDRGSLYVNG DQA1*05:01/DQB1*02:01 DQA1*05:01/DQB1*02:01 (DQ2), 14 (DQ2)DRB1*01:01, DRB1*03:01, DRB1*04:01, DRB1*04:02, DRB1*04:04, DRB1*04:05,DRB1*07:01, DRB1*08:02, DRB1*09:01, DRB1*11:04, DRB1*13:02, DRB1*15:01,DRB1*15:02 759 EELGPYTLDRNSLYVNG DRB1*03:01 DQA1*05:01/DQB1*02:01 (DQ2),12 DRB1*03:01, DRB1*04:01, DRB1*04:02,DRB1*04:04, DRB1*04:05, DRB1*07:01, DRB1*08:02, DRB1*09:01, DRB1*13:02,DRB1*15:01, DRB1*15:02 760 LKPLFKSTSVGPLYSG DRB1*11:04DQA1*05:01/DQB1*02:01 (DQ2), 16 DRB1*01:01, DRB1*03:01, DRB1*04:01,DRB1*04:02, DRB1*04:04, DRB1*04:05, DRB1*07:01, DRB1*08:02, DRB1*08:03,DRB1*09:01, DRB1*11:01, DRB1*11:04, DRB1*13:01, DRB1*13:02, DRB1*15:01764 FDKAFTAATTEVSRTE DQA1*05:01/DQB1*03:01  DQA1*05:01/DQB1*03:01 (DQ7), 9 (DQ7) DRB1*01:01, DRB1*04:01, DRB1*04:04,DRB1*04:05, DRB1*07:01, DRB1*09:01, DRB1*11:01, DRB1*15:01 765ELGPYTLDRDSLYVN DQA1*05:01/DQB1*02:01  DQA1*05:01/DQB1*02:01 (DQ2), 11(DQ2) DRB1*03:01, DRB1*04:01, DRB1*04:02,DRB1*04:04, DRB1*04:05, DRB1*07:01, DRB1*08:02, DRB1*13:02, DRB1*15:01,DRB1*15:02 766 GLLKPLFKSTSVGPL DRB1*11:04 DQA1*05:01/DQB1*02:01 (DQ2),16 DRB1*01:01, DRB1*03:01, DRB1*04:01,DRB1*04:02, DRB1*04:04, DRB1*04:05, DRB1*07:01, DRB1*08:02, DRB1*08:03,DRB1*09:01, DRB1*11:01, DRB1*11:04, DRB1*13:01, DRB1*13:02, DRB1*15:01768 SDPYKATSAVVITST DQA1*05:01/DQB1*03:01  DQA1*05:01/DQB1*02:01 (DQ2),10 (DQ7) DQA1*05:01/DQB1*03:01 (DQ7),DQB1*06:02, DRB1*01:01, DRB1*04:01, DRB1*04:04, DRB1*07:01, DRB1*09:01,DRB1*15:01, DRB1*15:02 770 SRKFNTMESVLQGLL DRB1*09:01DQA1*05:01/DQB1*03:01 (DQ7), 10 DRB1*01:01, DRB1*03:01, DRB1*04:01,DRB1*04:04, DRB1*04:05, DRB1*07:01, DRB1*09:01, DRB1*13:02, DRB1*15:01

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The invention claimed is:
 1. A method for killing target cells in apatient who has cancer, comprising administering to the patient aneffective number of activated T cells that selectively recognize acancer cell, which presents a peptide consisting of the amino acidsequence of MIPTFTALL (SEQ ID NO: 1), wherein the cancer is selectedfrom the group consisting of ovarian cancer, colorectal cancer,gallbladder cancer, non-Hodgkin lymphoma, non-small cell lung cancer,and uterine and endometrial cancer.
 2. The method of claim 1, whereinthe T cells are autologous to the patient.
 3. The method of claim 1,wherein the T cells are obtained from a healthy donor.
 4. The method ofclaim 1, wherein the T cells are obtained from tumor infiltratinglymphocytes or peripheral blood mononuclear cells.
 5. The method ofclaim 1, wherein the activated T cells are expanded in vitro.
 6. Themethod of claim 1, wherein the population of activated T cells areadministered in the form of a composition.
 7. The method of claim 6,wherein the composition further comprises an adjuvant.
 8. The method ofclaim 7, wherein the adjuvant is selected from anti-CD40 antibody,imiquimod, resiquimod, GM-CSF, cyclophosphamide, sunitinib, bevacizumab,interferon-alpha, interferon-beta, CpG oligonucleotides and derivatives,poly-(I:C) and derivatives, RNA, sildenafil, particulate formulationswith poly(lactide co-glycolide) (PLG), virosomes, interleukin (IL)-1,IL-2, IL-4, IL-7, IL-12, IL-13, IL-15, IL-21, and IL-23.
 9. The methodof claim 1, wherein the activated T cells are cytotoxic T cells producedby contacting T cells with an antigen presenting cell that presents thepeptide in a complex with an MHC class I molecule on the surface of theantigen presenting cell, for a period of time sufficient to activatesaid T cell.
 10. The method of claim 9, wherein the antigen presentingcell is infected with a recombinant virus expressing the peptide. 11.The method of claim 10, wherein the antigen presenting cell is adendritic cell or a macrophage.
 12. The method of claim 5, wherein theexpansion is in the presence of an anti-CD28 antibody and IL-12.
 13. Themethod of claim 1, wherein the population of activated T cells comprisesCD8-positive cells.
 14. The method of claim 9, wherein the contacting isin vitro.
 15. The method of claim 1, wherein the cancer is ovariancancer.
 16. The method of claim 1, wherein the cancer is colorectalcancer.
 17. The method of claim 1, wherein the cancer is gallbladdercancer.
 18. The method of claim 1, wherein the cancer is non-Hodgkinlymphoma.
 19. The method of claim 1, wherein the cancer is non-smallcell lung cancer.
 20. The method of claim 1, wherein the cancer isuterine and endometrial cancer.